ISDA: 7OSM

Deposition Date 2021-06-09

Release Date 2021-12-08

Last Version Date 2024-01-31

Entry Detail

PDB ID:

7OSM

Keywords:

RIBOSOME

Title:

Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands

Biological Source:

Source Organism:

Saccharomyces cerevisiae (Taxon ID: 4932)
Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.00 Å

R-Value Free:

0.28

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:TA (auth: 18S)
Chain Length:1798
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:A (auth: 25S)
Chain Length:3396
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C (auth: 58S)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B (auth: AB)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:PHE tRNA
Chain IDs:BC (auth: ASIT)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:FMET tRNA
Chain IDs:CC (auth: PSIT)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:BJ4_G0022010.mRNA.1.CDS.1
Chain IDs:YB (auth: RACK)
Chain Length:319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:Elongation factor 2
Chain IDs:AC (auth: eEF2)
Chain Length:842
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:O (auth: eL13)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:P (auth: eL14)
Chain Length:138
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P36105 Pfam ID:PF00467, PF01929

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:Q (auth: eL15)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05748 Pfam ID:PF00827

Polymer Type:polypeptide(L)
Molecule:BJ4_G0033900.mRNA.1.CDS.1
Chain IDs:T (auth: eL18)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:U (auth: eL19)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX82 Pfam ID:PF01280

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Chain IDs:V (auth: eL20)
Chain Length:172
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0003770.mRNA.1.CDS.1
Chain IDs:W (auth: eL21)
Chain Length:160
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Chain IDs:X (auth: eL22)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Chain IDs:Z (auth: eL24)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Chain IDs:CA (auth: eL27)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:EA (auth: eL29)
Chain Length:59
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0020000.mRNA.1.CDS.1
Chain IDs:FA (auth: eL30)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0008090.mRNA.1.CDS.1
Chain IDs:GA (auth: eL31)
Chain Length:113
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:HN1_G0013350.mRNA.1.CDS.1
Chain IDs:HA (auth: eL32)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0025510.mRNA.1.CDS.1
Chain IDs:IA (auth: eL33)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Chain IDs:JA (auth: eL34)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:LA (auth: eL36)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05745 Pfam ID:PF01158

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Chain IDs:MA (auth: eL37)
Chain Length:88
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0032190.mRNA.1.CDS.1
Chain IDs:NA (auth: eL38)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:OA (auth: eL39)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Chain IDs:PA (auth: eL40)
Chain Length:128
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:eL41
Chain IDs:QA (auth: eL41)
Chain Length:25
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0001880.mRNA.1.CDS.1
Chain IDs:RA (auth: eL42)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:SA (auth: eL43)
Chain Length:92
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX25 Pfam ID:PF01780

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Chain IDs:I (auth: eL6)
Chain Length:176
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:K (auth: eL8)
Chain Length:256
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P17076 Pfam ID:PF01248

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1
Chain IDs:VA (auth: eS1)
Chain Length:255
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Chain IDs:EB (auth: eS10)
Chain Length:105
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0020710.mRNA.1.CDS.1
Chain IDs:KB (auth: eS17)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Chain IDs:MB (auth: eS19)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Chain IDs:OB (auth: eS21)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Chain IDs:RB (auth: eS24)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Chain IDs:SB (auth: eS25)
Chain Length:108
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Chain IDs:TB (auth: eS26)
Chain Length:119
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:UB (auth: eS27)
Chain Length:82
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P35997 Pfam ID:PF01667

Polymer Type:polypeptide(L)
Molecule:eS28
Chain IDs:VB (auth: eS28)
Chain Length:67
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Chain IDs:XB (auth: eS30)
Chain Length:63
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Chain IDs:ZB (auth: eS31)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Chain IDs:YA (auth: eS4)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Chain IDs:AB (auth: eS6)
Chain Length:236
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Chain IDs:BB (auth: eS7)
Chain Length:190
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Chain IDs:CB (auth: eS8)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:DC (auth: mRNA)
Chain Length:8
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:D (auth: uL10)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12-B
Chain IDs:EC (auth: uL11)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Chain IDs:R (auth: uL13)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-B
Chain IDs:Y (auth: uL14)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:DA (auth: uL15)
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Chain IDs:M (auth: uL16)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:H (auth: uL18)
Chain Length:297
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-B
Chain IDs:E (auth: uL2)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0005750.mRNA.1.CDS.1
Chain IDs:S (auth: uL22)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Chain IDs:AA (auth: uL23)
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 L26-A
Gene (Uniprot):RPL26A
Chain IDs:BA (auth: uL24)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05743 Pfam ID:PF16906, PF00467

Polymer Type:polypeptide(L)
Molecule:BJ4_G0044250.mRNA.1.CDS.1
Chain IDs:KA (auth: uL29)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Chain IDs:F (auth: uL3)
Chain Length:387
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Chain IDs:J (auth: uL30)
Chain Length:244
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0008850.mRNA.1.CDS.1
Chain IDs:G (auth: uL4)
Chain Length:362
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0027750.mRNA.1.CDS.1
Chain IDs:N (auth: uL5)
Chain Length:174
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:L (auth: uL6)
Chain Length:191
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05738 Pfam ID:PF00347

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Chain IDs:NB (auth: uS10)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-A
Chain IDs:HB (auth: uS11)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Chain IDs:QB (auth: uS12)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-B
Chain IDs:LB (auth: uS13)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:HLJ1_G0030400.mRNA.1.CDS.1
Chain IDs:WB (auth: uS14)
Chain Length:56
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:GB (auth: uS15)
Chain Length:151
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-B
Chain IDs:FB (auth: uS17)
Chain Length:156
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:IB (auth: uS19)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0
Chain IDs:UA (auth: uS2)
Chain Length:252
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0045400.mRNA.1.CDS.1
Chain IDs:XA (auth: uS3)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0026100.mRNA.1.CDS.1
Chain IDs:DB (auth: uS4)
Chain Length:197
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:WA (auth: uS5)
Chain Length:254
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Rps5p
Gene (Uniprot):RPS5
Chain IDs:ZA (auth: uS7)
Chain Length:225
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:A0A1L4AA68 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Chain IDs:PB (auth: uS8)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polypeptide(L)
Molecule:BJ4_G0008010.mRNA.1.CDS.1
Chain IDs:JB (auth: uS9)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
DDE	AC	HIS	modified residue

Ligand Molecules

GTP

Primary Citation

Accuracy mechanism of eukaryotic ribosome translocation.

Djumagulov, M, Demeshkina, N, Jenner, L, Rozov, A, Yusupov, M, Yusupova, G, Adams, P.D.Show

Nature 600 543 546 (2021)

PMID: 34853469 DOI: 10.1038/s41586-021-04131-9

Abstact

Translation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy1. Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon-anticodon interactions involving diphthamide1 and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy2. The model demonstrates how the decoding centre releases a codon-anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a 'pawl' defining the directionality of translocation3. This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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