› 4v4b

Electron Microscopy
11.7Å resolution

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.

Released:
DOI: 10.2210/pdb4v4b/pdb
PDB entry 4v4b coloured by chain, front view.
PDB entry 4v4b coloured by chain, side view.
PDB entry 4v4b coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jørgensen R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP, Frank J
EMBO J 23 1008-19 (2004)
PMID: 14976550
Related structures: EMD-1067

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
PDBe Complex ID:
PDB-CPX-126841 (preferred)
Entry contents:
44 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (47 distinct):
Elongation factor 2 Chain: AT
Molecule details ›
Chain: AT
Length: 842 amino acids
Theoretical weight: 93.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32324 (Residues: 1-842; Coverage: 100%)
Gene names: EFT1, EFT2, O3317, YDR385W, YOR133W, YOR3317W
Sequence domains:
Small ribosomal subunit protein uS2A Chain: AB
Molecule details ›
Chain: AB
Length: 185 amino acids
Theoretical weight: 20.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32905 (Residues: 14-198; Coverage: 73%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: AC
Molecule details ›
Chain: AC
Length: 192 amino acids
Theoretical weight: 21.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05750 (Residues: 2-193; Coverage: 80%)
Gene names: N1653, RPS3, SUF14, YNL178W
Sequence domains:
Small ribosomal subunit protein uS4A Chain: AD
Molecule details ›
Chain: AD
Length: 179 amino acids
Theoretical weight: 20.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 19-197; Coverage: 91%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AE
Molecule details ›
Chain: AE
Length: 149 amino acids
Theoretical weight: 15.64 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 75-223; Coverage: 59%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
Small ribosomal subunit protein uS7 Chain: AG
Molecule details ›
Chain: AG
Length: 150 amino acids
Theoretical weight: 16.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26783 (Residues: 76-225; Coverage: 67%)
Gene names: J2045, RPS2, RPS5, YJR123W
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S22 Chain: AH
Molecule details ›
Chain: AH
Length: 129 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae
40S ribosomal protein S16 Chain: AI
Molecule details ›
Chain: AI
Length: 142 amino acids
Theoretical weight: 15.75 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein uS10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 100 amino acids
Theoretical weight: 11.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38701 (Residues: 21-121; Coverage: 83%)
Gene names: RPS20, URP2, YHL015W
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11A Chain: AK
Molecule details ›
Chain: AK
Length: 136 amino acids
Theoretical weight: 14.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06367 (Residues: 2-137; Coverage: 99%)
Gene names: CRY1, RPL59, RPS14A, YCR031C, YCR31C
Sequence domains: Ribosomal protein S11
40S ribosomal protein S23 Chain: AL
Molecule details ›
Chain: AL
Length: 118 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae
40S ribosomal protein S18 Chain: AM
Molecule details ›
Chain: AM
Length: 132 amino acids
Theoretical weight: 15.49 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein uS14B Chain: AN
Molecule details ›
Chain: AN
Length: 36 amino acids
Theoretical weight: 4.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41058 (Residues: 21-56; Coverage: 64%)
Gene names: RPS29B, RPS36B, YDL061C, YS29B
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
Length: 65 amino acids
Theoretical weight: 7.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 66-130; Coverage: 43%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains: Ribosomal protein S15
40S ribosomal protein S11 Chain: AQ
Molecule details ›
Chain: AQ
Length: 76 amino acids
Theoretical weight: 8.78 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein uS19 Chain: AS
Molecule details ›
Chain: AS
Length: 80 amino acids
Theoretical weight: 8.9 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01855 (Residues: 47-126; Coverage: 56%)
Gene names: RPS15, RPS21, YOL040C
Sequence domains: Ribosomal protein S19
60S ribosomal protein L1 Chain: BA
Molecule details ›
Chain: BA
Length: 217 amino acids
Theoretical weight: 24.52 KDa
Source organism: Saccharomyces cerevisiae
60S ribosomal protein L2 Chain: BB
Molecule details ›
Chain: BB
Length: 253 amino acids
Theoretical weight: 27.33 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein uL3 Chain: BC
Molecule details ›
Chain: BC
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: 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 uL4B Chain: BD
Molecule details ›
Chain: BD
Length: 361 amino acids
Theoretical weight: 39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49626 (Residues: 2-362; Coverage: 100%)
Gene names: RPL2B, RPL4B, YD8119.17, YDR012W
Sequence domains:
Large ribosomal subunit protein uL18 Chain: BE
Molecule details ›
Chain: BE
Length: 222 amino acids
Theoretical weight: 25.44 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26321 (Residues: 11-232; Coverage: 75%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Large ribosomal subunit protein uL30A Chain: BF
Molecule details ›
Chain: BF
Length: 162 amino acids
Theoretical weight: 18.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05737 (Residues: 83-244; Coverage: 66%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein eL8A Chain: BG
Molecule details ›
Chain: BG
Length: 119 amino acids
Theoretical weight: 12.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17076 (Residues: 102-220; Coverage: 47%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6A Chain: BH
Molecule details ›
Chain: BH
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: 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 Chain: BI
Molecule details ›
Chain: BI
Length: 168 amino acids
Theoretical weight: 19.25 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41805 (Residues: 1-168; Coverage: 76%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
60S ribosomal protein L11 Chain: BJ
Molecule details ›
Chain: BJ
Length: 173 amino acids
Theoretical weight: 19.62 KDa
Source organism: Saccharomyces cerevisiae
60S ribosomal protein L12 Chain: BK
Molecule details ›
Chain: BK
Length: 131 amino acids
Theoretical weight: 13.95 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL15A Chain: BL
Molecule details ›
Chain: BL
Length: 203 amino acids
Theoretical weight: 24.35 KDa
Source organism: 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 Chain: BM
Molecule details ›
Chain: BM
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26784 (Residues: 2-147; Coverage: 73%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: BN
Molecule details ›
Chain: BN
Length: 183 amino acids
Theoretical weight: 20.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05740 (Residues: 2-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
60S ribosomal protein L18 Chain: BO
Molecule details ›
Chain: BO
Length: 120 amino acids
Theoretical weight: 13.13 KDa
Source organism: Saccharomyces cerevisiae
60S ribosomal protein L19 Chain: BP
Molecule details ›
Chain: BP
Length: 142 amino acids
Theoretical weight: 16.32 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL21A Chain: BQ
Molecule details ›
Chain: BQ
Length: 100 amino acids
Theoretical weight: 11.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02753 (Residues: 1-100; Coverage: 63%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L23 Chain: BR
Molecule details ›
Chain: BR
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL24A Chain: BS
Molecule details ›
Chain: BS
Length: 56 amino acids
Theoretical weight: 6.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04449 (Residues: 1-56; Coverage: 36%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: BT
Molecule details ›
Chain: BT
Length: 83 amino acids
Theoretical weight: 9.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04456 (Residues: 60-142; Coverage: 59%)
Gene names: RPL25, YOL127W
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24A Chain: BU
Molecule details ›
Chain: BU
Length: 126 amino acids
Theoretical weight: 14.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05743 (Residues: 2-127; Coverage: 99%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein uL15 Chain: BV
Molecule details ›
Chain: BV
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: 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 eL32 Chain: B0
Molecule details ›
Chain: B0
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
60S ribosomal protein L31 Chain: BW
Molecule details ›
Chain: BW
Length: 112 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae
60S ribosomal protein L35 Chain: BX
Molecule details ›
Chain: BX
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL37A Chain: BY
Molecule details ›
Chain: BY
Length: 87 amino acids
Theoretical weight: 9.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49166 (Residues: 2-88; Coverage: 99%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L42 Chain: BZ
Molecule details ›
Chain: BZ
Length: 105 amino acids
Theoretical weight: 12.12 KDa
Source organism: Saccharomyces cerevisiae
60S ribosomal protein L43 Chain: B9
Molecule details ›
Chain: B9
Length: 91 amino acids
Theoretical weight: 9.98 KDa
Source organism: Saccharomyces cerevisiae
18S Ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1507 nucleotides
Theoretical weight: 489.33 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
5.8S/25S ribosomal RNA Chain: B3
Molecule details ›
Chain: B3
Length: 2999 nucleotides
Theoretical weight: 971.01 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5S ribosomal RNA Chain: B4
Molecule details ›
Chain: B4
Length: 125 nucleotides
Theoretical weight: 40.3 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 11.7Å
Relevant EMDB volumes: EMD-1067

Quick links

Citations

60 review citations

Regulation of translation initiation in eukaryotes: mechanisms and biological targets.
Sonenberg et al. (2009)
59 more

1 mention without citation

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
Hassan et al. (2023)