› 5mei

X-ray diffraction
3.5Å resolution

Crystal structure of Agelastatin A bound to the 80S ribosome

Released:
DOI: 10.2210/pdb5mei/pdb
PDB entry 5mei coloured by chain, front view.
PDB entry 5mei coloured by chain, side view.
PDB entry 5mei coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Inhibition of Eukaryotic Translation by the Antitumor Natural Product Agelastatin A.
McClary B, Zinshteyn B, Meyer M, Jouanneau M, Pellegrino S, Yusupova G, Schuller A, Reyes JCP, Lu J, Guo Z, Ayinde S, Luo C, Dang Y, Romo D, Yusupov M, Green R, Liu JO
Cell Chem Biol 24 605-613.e5 (2017)
PMID: 28457705

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero 79-mer
hetero 80-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219102 (preferred)
Entry contents:
79 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (83 distinct):
Large ribosomal subunit protein uL2A Chains: CD, j
Molecule details ›
Chains: CD, j
Length: 252 amino acids
Theoretical weight: 27.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX45 (Residues: 2-253; Coverage: 99%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein uL3 Chains: CE, k
Molecule details ›
Chains: CE, k
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14126 (Residues: 2-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chains: CF, l
Molecule details ›
Chains: CF, l
Length: 361 amino acids
Theoretical weight: 39.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10664 (Residues: 2-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein uL18 Chains: CG, m
Molecule details ›
Chains: CG, m
Length: 296 amino acids
Theoretical weight: 33.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26321 (Residues: 2-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
Large ribosomal subunit protein eL6A Chains: CH, n
Molecule details ›
Chains: CH, n
Length: 175 amino acids
Theoretical weight: 19.87 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02326 (Residues: 2-176; Coverage: 99%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30A Chains: CI, o
Molecule details ›
Chains: CI, o
Length: 222 amino acids
Theoretical weight: 25.24 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05737 (Residues: 23-244; Coverage: 91%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein eL8A Chains: CJ, p
Molecule details ›
Chains: CJ, p
Length: 233 amino acids
Theoretical weight: 25.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17076 (Residues: 24-256; Coverage: 91%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chains: CK, q
Molecule details ›
Chains: CK, q
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL16 Chains: CL, r
Molecule details ›
Chains: CL, r
Length: 220 amino acids
Theoretical weight: 25.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41805 (Residues: 2-221; Coverage: 100%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5B Chains: CM, s
Molecule details ›
Chains: CM, s
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E757 (Residues: 6-174; Coverage: 97%)
Gene names: RP39B, RPL11B, RPL16B, YGR085C
Sequence domains:
Large ribosomal subunit protein eL13A Chains: CN, t
Molecule details ›
Chains: CN, t
Length: 193 amino acids
Theoretical weight: 21.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12690 (Residues: 2-194; Coverage: 97%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14A Chains: CO, u
Molecule details ›
Chains: CO, u
Length: 136 amino acids
Theoretical weight: 14.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36105 (Residues: 3-138; Coverage: 99%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL15A Chains: CP, v
Molecule details ›
Chains: CP, v
Length: 203 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05748 (Residues: 2-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chains: CQ, w
Molecule details ›
Chains: CQ, w
Length: 197 amino acids
Theoretical weight: 22.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26784 (Residues: 3-199; Coverage: 99%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chains: CR, x
Molecule details ›
Chains: CR, x
Length: 183 amino acids
Theoretical weight: 20.46 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05740 (Residues: 2-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chains: CS, y
Molecule details ›
Chains: CS, y
Length: 185 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX49 (Residues: 2-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19A Chains: CT, z
Molecule details ›
Chains: CT, z
Length: 188 amino acids
Theoretical weight: 21.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX82 (Residues: 2-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20A Chains: 0, CU
Molecule details ›
Chains: 0, CU
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21A Chains: 2, CV
Molecule details ›
Chains: 2, CV
Length: 159 amino acids
Theoretical weight: 18.15 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02753 (Residues: 2-160; Coverage: 99%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22A Chains: 5, CW
Molecule details ›
Chains: 5, CW
Length: 100 amino acids
Theoretical weight: 11.26 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05749 (Residues: 9-108; Coverage: 83%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL14A Chains: CX, l2
Molecule details ›
Chains: CX, l2
Length: 136 amino acids
Theoretical weight: 14.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX41 (Residues: 2-137; Coverage: 99%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24A Chains: 7, CY
Molecule details ›
Chains: 7, CY
Length: 98 amino acids
Theoretical weight: 11.37 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04449 (Residues: 1-98; Coverage: 63%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chains: 8, CZ
Molecule details ›
Chains: 8, CZ
Length: 121 amino acids
Theoretical weight: 13.77 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04456 (Residues: 22-142; Coverage: 85%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL24A Chains: 9, DA
Molecule details ›
Chains: 9, DA
Length: 126 amino acids
Theoretical weight: 14.13 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05743 (Residues: 2-127; Coverage: 99%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein eL27A Chains: AA, DB
Molecule details ›
Chains: AA, DB
Length: 135 amino acids
Theoretical weight: 15.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H6 (Residues: 2-136; Coverage: 99%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein uL15 Chains: AB, DC
Molecule details ›
Chains: AB, DC
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02406 (Residues: 2-149; Coverage: 99%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chains: AC, DD
Molecule details ›
Chains: AC, DD
Length: 58 amino acids
Theoretical weight: 6.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05747 (Residues: 2-59; Coverage: 98%)
Gene names: RPL29, YFR032BW, YFR032C-A, YL43
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL30 Chains: AD, DE
Molecule details ›
Chains: AD, DE
Length: 97 amino acids
Theoretical weight: 10.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14120 (Residues: 9-105; Coverage: 92%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL31A Chains: AE, DF
Molecule details ›
Chains: AE, DF
Length: 109 amino acids
Theoretical weight: 12.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H8 (Residues: 4-112; Coverage: 97%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chains: AF, DG
Molecule details ›
Chains: AF, DG
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38061 (Residues: 2-128; Coverage: 98%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33A Chains: AG, DH
Molecule details ›
Chains: AG, DH
Length: 106 amino acids
Theoretical weight: 12.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05744 (Residues: 2-107; Coverage: 99%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34A Chains: AH, DI
Molecule details ›
Chains: AH, DI
Length: 112 amino acids
Theoretical weight: 12.61 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P87262 (Residues: 2-113; Coverage: 93%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29A Chains: AI, DJ
Molecule details ›
Chains: AI, DJ
Length: 119 amino acids
Theoretical weight: 13.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX84 (Residues: 2-120; Coverage: 99%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chains: AJ, DK
Molecule details ›
Chains: AJ, DK
Length: 99 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05745 (Residues: 2-100; Coverage: 99%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chains: AK, DL
Molecule details ›
Chains: AK, DL
Length: 87 amino acids
Theoretical weight: 9.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49166 (Residues: 2-88; Coverage: 99%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chains: AL, DM
Molecule details ›
Chains: AL, DM
Length: 77 amino acids
Theoretical weight: 8.71 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49167 (Residues: 2-78; Coverage: 99%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chains: AM, DN
Molecule details ›
Chains: AM, DN
Length: 50 amino acids
Theoretical weight: 6.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04650 (Residues: 2-51; Coverage: 98%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL40A Chains: AN, DO
Molecule details ›
Chains: AN, DO
Length: 52 amino acids
Theoretical weight: 6.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CH08 (Residues: 77-128; Coverage: 41%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains: Ribosomal L40e family
Small ribosomal subunit protein eS32A Chains: AO, DP
Molecule details ›
Chains: AO, DP
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)
Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL42A Chains: AP, DQ
Molecule details ›
Chains: AP, DQ
Length: 105 amino acids
Theoretical weight: 12.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX27 (Residues: 2-106; Coverage: 99%)
Gene names: N1722, RPL41A, RPL42A, SCL41A, YNL162W
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43A Chains: AQ, DR
Molecule details ›
Chains: AQ, DR
Length: 91 amino acids
Theoretical weight: 9.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX25 (Residues: 2-92; Coverage: 99%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Suppressor protein STM1 Chain: i
Molecule details ›
Chain: i
Length: 168 amino acids
Theoretical weight: 18.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39015 (Residues: 9-176; Coverage: 62%)
Gene names: L9634.1, MPT4, STM1, STO1, YLR150W
Sequence domains: Stm1
Large ribosomal subunit protein uL10 Chain: p0
Molecule details ›
Chain: p0
Length: 220 amino acids
Theoretical weight: 24.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05317 (Residues: 2-221; Coverage: 71%)
Gene names: L10E, L8300.8, RPA0, RPL10E, RPLA0, RPP0, YLR340W
Sequence domains:
Suppressor protein STM1 Chain: sM
Molecule details ›
Chain: sM
Length: 104 amino acids
Theoretical weight: 10.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39015 (Residues: 23-85; Coverage: 23%)
Gene names: L9634.1, MPT4, STM1, STO1, YLR150W
Sequence domains: Stm1
Small ribosomal subunit protein uS2A Chains: B, s0
Molecule details ›
Chains: B, s0
Length: 206 amino acids
Theoretical weight: 22.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32905 (Residues: 2-207; Coverage: 82%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1A Chains: C, s1
Molecule details ›
Chains: C, s1
Length: 216 amino acids
Theoretical weight: 24.5 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33442 (Residues: 20-235; Coverage: 85%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chains: D, s2
Molecule details ›
Chains: D, s2
Length: 217 amino acids
Theoretical weight: 23.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 34-250; Coverage: 85%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
Small ribosomal subunit protein uS3 Chains: E, s3
Molecule details ›
Chains: E, s3
Length: 223 amino acids
Theoretical weight: 24.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05750 (Residues: 3-225; Coverage: 93%)
Gene names: N1653, RPS3, SUF14, YNL178W
Sequence domains:
Small ribosomal subunit protein eS4A Chains: F, s4
Molecule details ›
Chains: F, s4
Length: 260 amino acids
Theoretical weight: 29.34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX35 (Residues: 2-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Small ribosomal subunit protein uS7 Chains: G, s5
Molecule details ›
Chains: G, s5
Length: 206 amino acids
Theoretical weight: 22.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26783 (Residues: 20-225; Coverage: 92%)
Gene names: J2045, RPS2, RPS5, YJR123W
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS6A Chains: H, s6
Molecule details ›
Chains: H, s6
Length: 226 amino acids
Theoretical weight: 25.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX37 (Residues: 1-226; Coverage: 96%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chains: I, s7
Molecule details ›
Chains: I, s7
Length: 186 amino acids
Theoretical weight: 21.16 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26786 (Residues: 2-187; Coverage: 98%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8A Chains: J, s8
Molecule details ›
Chains: J, s8
Length: 199 amino acids
Theoretical weight: 22.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX39 (Residues: 2-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4A Chains: K, s9
Molecule details ›
Chains: K, s9
Length: 185 amino acids
Theoretical weight: 21.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 2-186; Coverage: 94%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein eS10A Chains: L, c0
Molecule details ›
Chains: L, c0
Length: 105 amino acids
Theoretical weight: 12.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08745 (Residues: 1-105; Coverage: 100%)
Gene names: RPS10A, YOR293W
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17A Chains: M, c1
Molecule details ›
Chains: M, c1
Length: 155 amino acids
Theoretical weight: 17.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX47 (Residues: 2-156; Coverage: 99%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Small ribosomal subunit protein eS12 Chains: N, c2
Molecule details ›
Chains: N, c2
Length: 124 amino acids
Theoretical weight: 13.33 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P48589 (Residues: 20-143; Coverage: 87%)
Gene names: RPS12, YOR369C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chains: O, c3
Molecule details ›
Chains: O, c3
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 2-151; Coverage: 99%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Small ribosomal subunit protein uS11B Chains: P, c4
Molecule details ›
Chains: P, c4
Length: 128 amino acids
Theoretical weight: 13.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39516 (Residues: 11-138; Coverage: 93%)
Gene names: CRY2, J0354, RPS14B, YJL191W
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS19 Chains: Q, c5
Molecule details ›
Chains: Q, c5
Length: 141 amino acids
Theoretical weight: 15.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01855 (Residues: 2-142; Coverage: 99%)
Gene names: RPS15, RPS21, YOL040C
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9A Chains: R, c6
Molecule details ›
Chains: R, c6
Length: 142 amino acids
Theoretical weight: 15.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX51 (Residues: 2-143; Coverage: 99%)
Gene names: RP61R, RPS16A, YM9375.12, YMR143W
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17B Chain: S
Molecule details ›
Chain: S
Length: 125 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14127 (Residues: 2-126; Coverage: 92%)
Gene names: RP51B, RPS17B, YDR447C
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13A Chains: T, c8
Molecule details ›
Chains: T, c8
Length: 145 amino acids
Theoretical weight: 16.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX55 (Residues: 2-146; Coverage: 99%)
Gene names: D9461.35, RPS18A, YDR450W
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19A Chains: U, c9
Molecule details ›
Chains: U, c9
Length: 143 amino acids
Theoretical weight: 15.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07280 (Residues: 2-144; Coverage: 99%)
Gene names: RP55A, RPS16AA, RPS19A, YOL121C
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chains: V, d0
Molecule details ›
Chains: V, d0
Length: 110 amino acids
Theoretical weight: 12.58 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38701 (Residues: 12-121; Coverage: 91%)
Gene names: RPS20, URP2, YHL015W
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21A Chains: W, d1
Molecule details ›
Chains: W, d1
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)
Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8A Chains: X, d2
Molecule details ›
Chains: X, d2
Length: 129 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W1 (Residues: 2-130; Coverage: 99%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12A Chains: Y, d3
Molecule details ›
Chains: Y, d3
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX29 (Residues: 2-145; Coverage: 99%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24A Chains: Z, d4
Molecule details ›
Chains: Z, d4
Length: 134 amino acids
Theoretical weight: 15.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX31 (Residues: 2-135; Coverage: 99%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25A Chains: a, d5
Molecule details ›
Chains: a, d5
Length: 70 amino acids
Theoretical weight: 8 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E792 (Residues: 36-105; Coverage: 65%)
Gene names: RPS25A, RPS31A, YGR027C
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS26B Chains: b, d6
Molecule details ›
Chains: b, d6
Length: 97 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P39939 (Residues: 2-98; Coverage: 82%)
Gene names: RPS26B, YER131W
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS27A Chains: c, d7
Molecule details ›
Chains: c, d7
Length: 81 amino acids
Theoretical weight: 8.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35997 (Residues: 2-82; Coverage: 99%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28A Chains: d, d8
Molecule details ›
Chains: d, d8
Length: 63 amino acids
Theoretical weight: 7.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7X9 (Residues: 5-67; Coverage: 94%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14A Chains: d9, e
Molecule details ›
Chains: d9, e
Length: 53 amino acids
Theoretical weight: 6.34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41057 (Residues: 4-56; Coverage: 95%)
Gene names: L8084.11, RPS29A, RPS36A, YLR388W, YS29A
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS30A Chains: e0, f
Molecule details ›
Chains: e0, f
Length: 62 amino acids
Theoretical weight: 7.01 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX33 (Residues: 2-63; Coverage: 98%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS31 Chain: g
Molecule details ›
Chain: g
Length: 71 amino acids
Theoretical weight: 8.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05759 (Residues: 82-152; Coverage: 47%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chains: h, sR
Molecule details ›
Chains: h, sR
Length: 318 amino acids
Theoretical weight: 34.71 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38011 (Residues: 2-319; Coverage: 100%)
Gene names: ASC1, CPC2, YM9718.15C, YMR116C
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein eS17A Chain: c7
Molecule details ›
Chain: c7
Length: 121 amino acids
Theoretical weight: 13.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02407 (Residues: 2-122; Coverage: 89%)
Gene names: RP51A, RPS17A, YML024W
Sequence domains: Ribosomal S17
Small ribosomal subunit protein eS31 Chain: e1
Molecule details ›
Chain: e1
Length: 51 amino acids
Theoretical weight: 5.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05759 (Residues: 102-152; Coverage: 34%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains: Ribosomal protein S27a
25S ribosomal RNA Chains: 1, AR
Molecule details ›
Chains: 1, AR
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chains: 3, AS
Molecule details ›
Chains: 3, AS
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chains: 4, AT
Molecule details ›
Chains: 4, AT
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
18S Ribosomal RNA Chains: 6, A
Molecule details ›
Chains: 6, A
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand OHX 1070 x OHX
Ligand MG 1406 x MG
Ligand 7MB 2 x 7MB
Ligand ZN 16 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1, SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 304.08Å b: 286.55Å c: 436.55Å
α: 90° β: 99.05° γ: 90°
R-values:
R R work R free
0.196 0.195 0.239
Expression system: Saccharomyces cerevisiae

Quick links

Citations

4 review citations

Roadblocks and resolutions in eukaryotic translation.
Schuller et al. (2018)
3 more

2 mentions without citation

Inhibition of the Eukaryotic 80S Ribosome as a Potential Anticancer Therapy: A Structural Perspective.
Pellegrino et al. (2021)
1 more