› 5wyj

Electron Microscopy
8.7Å resolution

Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)

Released:
DOI: 10.2210/pdb5wyj/pdb
PDB entry 5wyj coloured by chain, front view.
PDB entry 5wyj coloured by chain, side view.
PDB entry 5wyj coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Molecular architecture of the 90S small subunit pre-ribosome.
Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K
Elife 6 (2017)
PMID: 28244370
Related structures: EMD-6695

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 64-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126852 (preferred)
Entry contents:
58 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (61 distinct):
rRNA 2'-O-methyltransferase fibrillarin Chains: 3B, 3C
Molecule details ›
Chains: 3B, 3C
Length: 327 amino acids
Theoretical weight: 34.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P15646 (Residues: 1-327; Coverage: 100%)
Gene names: D2870, LOT3, NOP1, YDL014W
Sequence domains: Fibrillarin
Nucleolar protein 56 Chain: 3D
Molecule details ›
Chain: 3D
Length: 504 amino acids
Theoretical weight: 56.96 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12460 (Residues: 1-504; Coverage: 100%)
Gene names: L8167.9, NOP56, SIK1, YLR197W
Sequence domains:
Nucleolar protein 58 Chain: 3E
Molecule details ›
Chain: 3E
Length: 511 amino acids
Theoretical weight: 57.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12499 (Residues: 1-511; Coverage: 100%)
Gene names: NOP5, NOP58, O6108, YOR310C
Sequence domains:
Ribosomal RNA-processing protein 9 Chain: 3F
Molecule details ›
Chain: 3F
Length: 573 amino acids
Theoretical weight: 65.15 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06506 (Residues: 1-573; Coverage: 100%)
Gene names: RRP9, YPR137W
Sequence domains: WD domain, G-beta repeat
13 kDa ribonucleoprotein-associated protein Chains: 3G, 3H
Molecule details ›
Chains: 3G, 3H
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39990 (Residues: 1-126; Coverage: 100%)
Gene names: SNU13, YEL026W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Utp4 Chain: AA
Molecule details ›
Chain: AA
Length: 776 amino acids
Theoretical weight: 66.06 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp5 Chain: AB
Molecule details ›
Chain: AB
Length: 643 amino acids
Theoretical weight: 54.74 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp8 Chain: AC
Molecule details ›
Chain: AC
Length: 713 amino acids
Theoretical weight: 60.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp9 Chain: AD
Molecule details ›
Chain: AD
Length: 575 amino acids
Theoretical weight: 48.95 KDa
Source organism: Saccharomyces cerevisiae S288C
U3 small nucleolar RNA-associated protein 10 Chain: AE
Molecule details ›
Chain: AE
Length: 1769 amino acids
Theoretical weight: 173.59 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P42945 (Residues: 1-808; Coverage: 46%)
Gene names: J0808, UTP10, YJL109C
Sequence domains: U3 small nucleolar RNA-associated protein 10
Utp15 Chain: AF
Molecule details ›
Chain: AF
Length: 513 amino acids
Theoretical weight: 43.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp17 Chain: AG
Molecule details ›
Chain: AG
Length: 896 amino acids
Theoretical weight: 76.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Ribosome biogenesis protein BMS1 Chain: B1
Molecule details ›
Chain: B1
Length: 1183 amino acids
Theoretical weight: 135.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08965 (Residues: 1-1183; Coverage: 100%)
Gene names: BMS1, YPL217C
Sequence domains:
Periodic tryptophan protein 2 Chain: BA
Molecule details ›
Chain: BA
Length: 923 amino acids
Theoretical weight: 104.1 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25635 (Residues: 1-923; Coverage: 100%)
Gene names: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C
Sequence domains:
U3 small nucleolar RNA-associated protein 12 Chain: BB
Molecule details ›
Chain: BB
Length: 943 amino acids
Theoretical weight: 106.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12220 (Residues: 1-943; Coverage: 100%)
Gene names: DIP2, L3116, L9233.1, UTP12, YLR129W
Sequence domains:
U3 small nucleolar RNA-associated protein 13 Chain: BC
Molecule details ›
Chain: BC
Length: 817 amino acids
Theoretical weight: 91.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05946 (Residues: 1-817; Coverage: 100%)
Gene names: UTP13, YLR222C
Sequence domains:
U3 small nucleolar RNA-associated protein 18 Chain: BD
Molecule details ›
Chain: BD
Length: 594 amino acids
Theoretical weight: 66.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40362 (Residues: 1-594; Coverage: 100%)
Gene names: HRE594, J1098, UTP18, YJL069C
Sequence domains: WD domain, G-beta repeat
U3 small nucleolar RNA-associated protein 21 Chain: BE
Molecule details ›
Chain: BE
Length: 939 amino acids
Theoretical weight: 104.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06078 (Residues: 1-939; Coverage: 100%)
Gene names: L8084.22, UTP21, YLR409C
Sequence domains:
Ribosomal RNA-processing protein 7 Chain: CA
Molecule details ›
Chain: CA
Length: 297 amino acids
Theoretical weight: 34.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25368 (Residues: 1-297; Coverage: 100%)
Gene names: RRP7, YCL031C, YCL184, YCL31C
Sequence domains:
U3 small nucleolar RNA-associated protein 22 Chain: CB
Molecule details ›
Chain: CB
Length: 1237 amino acids
Theoretical weight: 140.66 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53254 (Residues: 1-1237; Coverage: 100%)
Gene names: UTP22, YGR090W
Sequence domains:
Ribosomal RNA small subunit methyltransferase NEP1 Chains: E1, E2
Molecule details ›
Chains: E1, E2
Length: 252 amino acids
Theoretical weight: 27.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06287 (Residues: 1-252; Coverage: 100%)
Gene names: EMG1, L9470.5, NEP1, YLR186W
Sequence domains: EMG1/NEP1 methyltransferase
Essential nuclear protein 1 Chain: E3
Molecule details ›
Chain: E3
Length: 483 amino acids
Theoretical weight: 55.21 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38333 (Residues: 1-483; Coverage: 100%)
Gene names: ENP1, MEG1, YBR1635, YBR247C
Sequence domains: Bystin
Enp2 Chain: E4
Molecule details ›
Chain: E4
Length: 707 amino acids
Theoretical weight: 60.19 KDa
Source organism: Saccharomyces cerevisiae S288C
KRR1 small subunit processome component Chain: K1
Molecule details ›
Chain: K1
Length: 316 amino acids
Theoretical weight: 37.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25586 (Residues: 1-316; Coverage: 100%)
Gene names: KRR1, YCL059C, YCL59C
Sequence domains:
U3 small nucleolar ribonucleoprotein protein IMP3 Chain: MA
Molecule details ›
Chain: MA
Length: 183 amino acids
Theoretical weight: 21.93 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32899 (Residues: 1-183; Coverage: 100%)
Gene names: IMP3, YHR148W
Sequence domains:
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: MB
Molecule details ›
Chain: MB
Length: 290 amino acids
Theoretical weight: 33.54 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53941 (Residues: 1-290; Coverage: 100%)
Gene names: IMP4, N2353, YNL075W
Sequence domains: Brix domain
U3 small nucleolar RNA-associated protein MPP10 Chain: MC
Molecule details ›
Chain: MC
Length: 593 amino acids
Theoretical weight: 54.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P47083 (Residues: 429-593; Coverage: 28%)
Gene names: J1411, MPP10, YJR002W, YJR83.5
Pre-rRNA-processing protein PNO1 Chain: P1
Molecule details ›
Chain: P1
Length: 274 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q99216 (Residues: 1-274; Coverage: 100%)
Gene names: DIM2, O3513, PNO1, RRP20, YOR145C, YOR3513C
Sequence domains: Krr1 KH1 domain
RNA 3'-terminal phosphate cyclase-like protein Chain: R1
Molecule details ›
Chain: R1
Length: 367 amino acids
Theoretical weight: 40.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08096 (Residues: 1-367; Coverage: 100%)
Gene names: RCL1, RTC1, YOL010W
Sequence domains:
rRNA biogenesis protein RRP5 Chain: R2
Molecule details ›
Chain: R2
Length: 1729 amino acids
Theoretical weight: 193.41 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05022 (Residues: 1-1729; Coverage: 100%)
Gene names: FMI1, RRP5, YM9959.11C, YMR229C
Sequence domains: S1 RNA binding domain
Sof1 Chain: S1
Molecule details ›
Chain: S1
Length: 489 amino acids
Theoretical weight: 41.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein eS1A Chain: SC
Molecule details ›
Chain: SC
Length: 255 amino acids
Theoretical weight: 28.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33442 (Residues: 1-255; Coverage: 100%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein eS4A Chain: SF
Molecule details ›
Chain: SF
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX35 (Residues: 1-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Small ribosomal subunit protein uS7 Chain: SG
Molecule details ›
Chain: SG
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26783 (Residues: 1-225; Coverage: 100%)
Gene names: J2045, RPS2, RPS5, YJR123W
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS6A Chain: SH
Molecule details ›
Chain: SH
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX37 (Residues: 1-236; Coverage: 100%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chain: SI
Molecule details ›
Chain: SI
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26786 (Residues: 1-190; Coverage: 100%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8A Chain: SJ
Molecule details ›
Chain: SJ
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX39 (Residues: 1-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4A Chain: SK
Molecule details ›
Chain: SK
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O13516 (Residues: 1-197; Coverage: 100%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein uS17A Chain: SM
Molecule details ›
Chain: SM
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX47 (Residues: 1-156; Coverage: 100%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Small ribosomal subunit protein eS12 Chain: SN
Molecule details ›
Chain: SN
Length: 143 amino acids
Theoretical weight: 15.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48589 (Residues: 1-143; Coverage: 100%)
Gene names: RPS12, YOR369C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chain: SO
Molecule details ›
Chain: SO
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05756 (Residues: 1-151; Coverage: 100%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Small ribosomal subunit protein uS11A Chain: SP
Molecule details ›
Chain: SP
Length: 137 amino acids
Theoretical weight: 14.56 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P06367 (Residues: 1-137; Coverage: 100%)
Gene names: CRY1, RPL59, RPS14A, YCR031C, YCR31C
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS9A Chain: SR
Molecule details ›
Chain: SR
Length: 143 amino acids
Theoretical weight: 15.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX51 (Residues: 1-143; Coverage: 100%)
Gene names: RP61R, RPS16A, YM9375.12, YMR143W
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS8A Chain: SX
Molecule details ›
Chain: SX
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0W1 (Residues: 1-130; Coverage: 100%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12A Chain: SY
Molecule details ›
Chain: SY
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX29 (Residues: 1-145; Coverage: 100%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24A Chain: SZ
Molecule details ›
Chain: SZ
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX31 (Residues: 1-135; Coverage: 100%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27A Chain: Sc
Molecule details ›
Chain: Sc
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P35997 (Residues: 1-82; Coverage: 100%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28A Chain: Sd
Molecule details ›
Chain: Sd
Length: 67 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E7X9 (Residues: 1-67; Coverage: 100%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS30A Chain: Sf
Molecule details ›
Chain: Sf
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Ubiquitin-ribosomal protein eS31 fusion protein Chain: Sg
Molecule details ›
Chain: Sg
Length: 152 amino acids
Theoretical weight: 17.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05759 (Residues: 1-152; Coverage: 100%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains:
Utp7 Chain: U1
Molecule details ›
Chain: U1
Length: 554 amino acids
Theoretical weight: 47.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp11 Chain: U2
Molecule details ›
Chain: U2
Length: 250 amino acids
Theoretical weight: 21.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp20 Chain: U3
Molecule details ›
Chain: U3
Length: 2493 amino acids
Theoretical weight: 212.19 KDa
Source organism: Saccharomyces cerevisiae S288C
rRNA-processing protein FCF1 Chain: U4
Molecule details ›
Chain: U4
Length: 189 amino acids
Theoretical weight: 21.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05498 (Residues: 1-189; Coverage: 100%)
Gene names: D9651.9, FCF1, YDR339C
Sequence domains: Fcf1
Ribosome biogenesis protein UTP30 Chain: U5
Molecule details ›
Chain: U5
Length: 274 amino acids
Theoretical weight: 31.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36144 (Residues: 1-274; Coverage: 100%)
Gene names: UTP30, YKR060W
Sequence domains: Ribosomal protein L1p/L10e family
Helical domain protein Chain: UA
Molecule details ›
Chain: UA
Length: 1615 amino acids
Theoretical weight: 137.46 KDa
Source organism: Saccharomyces cerevisiae S288C
Helical domain protein Chain: UB
Molecule details ›
Chain: UB
Length: 987 amino acids
Theoretical weight: 84.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Unassigned helices Chain: UC
Molecule details ›
Chain: UC
Length: 1033 amino acids
Theoretical weight: 87.93 KDa
Source organism: Saccharomyces cerevisiae S288C
U3 RNA Chain: 3A
Molecule details ›
Chain: 3A
Length: 333 nucleotides
Theoretical weight: 106.5 KDa
Sequence domains: Fungal small nucleolar RNA U3
5ETS RNA Chain: 5A
Molecule details ›
Chain: 5A
Length: 700 nucleotides
Theoretical weight: 225.54 KDa
18S Ribosomal RNA Chain: SA
Molecule details ›
Chain: SA
Length: 1812 nucleotides
Theoretical weight: 583.64 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.7Å
Relevant EMDB volumes: EMD-6695

Quick links

Citations

23 review citations

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors.
Sáez-Vásquez et al. (2019)
22 more

10 mentions without citation

Assembly of the small ribosomal subunit in yeast: mechanism and regulation.
Chaker-Margot M. (2018)
9 more