4V4B image
Deposition Date 2004-01-06
Release Date 2014-07-09
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4V4B
Keywords:
RIBOSOME
Title:
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.
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
11.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V4B validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:1507
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:C (auth: AB)
Chain Length:185
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32905 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:D (auth: AC)
Chain Length:192
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05750 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:E (auth: AD)
Chain Length:179
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:F (auth: AE)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25443 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: AG)
Chain Length:150
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26783 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22
Chain IDs:H (auth: AH)
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Chain IDs:I (auth: AI)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:J (auth: AJ)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38701 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Gene (Uniprot):RPS14A
Chain IDs:K (auth: AK)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06367 Pfam ID:PF00411
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:L (auth: AL)
Chain Length:118
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Chain IDs:M (auth: AM)
Chain Length:132
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29-B
Gene (Uniprot):RPS29B
Chain IDs:N (auth: AN)
Chain Length:36
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41058 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:O (auth: AO)
Chain Length:65
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05756 Pfam ID:PF00312
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:P (auth: AQ)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:Q (auth: AS)
Chain Length:80
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01855 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor 2
Gene (Uniprot):EFT1, EFT2
Chain IDs:B (auth: AT)
Chain Length:842
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32324 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:PA (auth: B0)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Polymer Type:polyribonucleotide
Molecule:5.8S/25S ribosomal RNA
Chain IDs:R (auth: B3)
Chain Length:2999
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:S (auth: B4)
Chain Length:125
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43
Chain IDs:UA (auth: B9)
Chain Length:91
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1
Chain IDs:T (auth: BA)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Chain IDs:U (auth: BB)
Chain Length:253
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:V (auth: BC)
Chain Length:386
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-B
Gene (Uniprot):RPL4B
Chain IDs:W (auth: BD)
Chain Length:361
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49626 Pfam ID:PF00573, PF14374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:X (auth: BE)
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:Y (auth: BF)
Chain Length:162
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:Z (auth: BG)
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:AA (auth: BH)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:BA (auth: BI)
Chain Length:168
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41805 Pfam ID:PF00252
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Chain IDs:CA (auth: BJ)
Chain Length:173
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Chain IDs:DA (auth: BK)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:EA (auth: BL)
Chain Length:203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:FA (auth: BM)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:GA (auth: BN)
Chain Length:183
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Chain IDs:HA (auth: BO)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Chain IDs:IA (auth: BP)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:JA (auth: BQ)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Chain IDs:KA (auth: BR)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:LA (auth: BS)
Chain Length:56
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:MA (auth: BT)
Chain Length:83
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:NA (auth: BU)
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:OA (auth: BV)
Chain Length:148
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31
Chain IDs:QA (auth: BW)
Chain Length:112
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Chain IDs:RA (auth: BX)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:SA (auth: BY)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42
Chain IDs:TA (auth: BZ)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
NA
Primary Citation
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Embo J. 23 1008 1019 (2004)
PMID: 14976550 DOI: 10.1038/sj.emboj.7600102

Abstact

An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.

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Disease

Primary Citation of related structures
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