6GZ3 image
Deposition Date 2018-07-03
Release Date 2018-12-05
Last Version Date 2022-03-30
Entry Detail
PDB ID:
6GZ3
Keywords:
RIBOSOME
Title:
tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)
Biological Source:
Source Organism:
Enterobacteria phage SP6 (Taxon ID: 194966)
Oryctolagus cuniculus (Taxon ID: 9986)
Saccharomyces cerevisiae (Taxon ID: 4932)
Host Organism:
Enterobacteria phage SP6
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6GZ3 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:A (auth: A2)
Chain Length:3612
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:MA (auth: A3)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:NA (auth: A4)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:OA (auth: AA)
Chain Length:252
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TT27 Pfam ID:PF00181, PF03947
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL3
Chain IDs:PA (auth: AB)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL4
Chain IDs:QA (auth: AC)
Chain Length:103
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL18
Chain IDs:RA (auth: AD)
Chain Length:106
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL6
Chain IDs:SA (auth: AE)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL30
Chain IDs:TA (auth: AF)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL8
Chain IDs:UA (auth: AG)
Chain Length:234
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL6
Chain IDs:VA (auth: AH)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L10 (Predicted)
Gene (Uniprot):RPL10
Chain IDs:WA (auth: AI)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:B7NZQ2 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:XA (auth: AJ)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TUB8 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL10
Chain IDs:GC (auth: AK)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL13
Chain IDs:YA (auth: AL)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL14
Chain IDs:ZA (auth: AM)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:AB (auth: AN)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T0C1 Pfam ID:PF00827
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL13
Chain IDs:BB (auth: AO)
Chain Length:195
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL22
Chain IDs:CB (auth: AP)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL18
Chain IDs:DB (auth: AQ)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL19
Chain IDs:EB (auth: AR)
Chain Length:181
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL20
Chain IDs:FB (auth: AS)
Chain Length:175
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL21
Gene (Uniprot):RPL21
Chain IDs:GB (auth: AT)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SHQ2 Pfam ID:PF01157
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL22
Chain IDs:HB (auth: AU)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:IB (auth: AV)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T6D1 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL24
Gene (Uniprot):RPL24
Chain IDs:JB (auth: AW)
Chain Length:121
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SE28 Pfam ID:PF01246
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL23
Chain IDs:KB (auth: AX)
Chain Length:117
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:LB (auth: AY)
Chain Length:127
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SQH0 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:MB (auth: AZ)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TXF6 Pfam ID:PF00467, PF01777
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL15
Chain IDs:NB (auth: Aa)
Chain Length:252
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL29
Chain IDs:OB (auth: Ab)
Chain Length:394
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL30
Chain IDs:PB (auth: Ac)
Chain Length:103
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL31
Gene (Uniprot):RPL31
Chain IDs:QB (auth: Ad)
Chain Length:106
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SHG0 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL32
Gene (Uniprot):RPL32
Chain IDs:RB (auth: Ae)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TUN8 Pfam ID:PF01655
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL33
Chain IDs:SB (auth: Af)
Chain Length:109
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL34
Chain IDs:TB (auth: Ag)
Chain Length:234
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL29
Chain IDs:UB (auth: Ah)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL36
Chain IDs:VB (auth: Ai)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:WB (auth: Aj)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:U3KPD5 Pfam ID:PF01907
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL38
Chain IDs:XB (auth: Ak)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL39
Gene (Uniprot):RPL39
Chain IDs:YB (auth: Al)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SYU7 Pfam ID:PF00832
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL40
Chain IDs:ZB (auth: Am)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL41
Chain IDs:AC (auth: An)
Chain Length:203
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL42
Gene (Uniprot):RPL36A
Chain IDs:BC (auth: Ao)
Chain Length:195
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1T040 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL43
Gene (Uniprot):RPL37A
Chain IDs:CC (auth: Ap)
Chain Length:91
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SY53 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:FC (auth: Aq)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SMR7 Pfam ID:PF03946, PF00298
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL28
Chain IDs:DC (auth: At)
Chain Length:157
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):RPL10A
Chain IDs:EC (auth: Au)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SKZ8 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:E (auth: B1)
Chain Length:1708
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS2
Chain IDs:U (auth: BA)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:V (auth: BB)
Chain Length:212
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SS70 Pfam ID:PF01015
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS5
Chain IDs:W (auth: BC)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS3
Chain IDs:F (auth: BD)
Chain Length:220
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS4
Chain IDs:X (auth: BE)
Chain Length:257
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: BF)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TFM5 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:Y (auth: BG)
Chain Length:232
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TM55 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:Z (auth: BH)
Chain Length:183
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SVB0
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS8
Chain IDs:AA (auth: BI)
Chain Length:207
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S9 (Predicted)
Gene (Uniprot):RPS9
Chain IDs:BA (auth: BJ)
Chain Length:179
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:B7NZS8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS10
Chain IDs:H (auth: BK)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TPV3 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:CA (auth: BL)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TRM4 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:I (auth: BM)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SFR8 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS15
Gene (Uniprot):RPS13
Chain IDs:DA (auth: BN)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SP51 Pfam ID:PF08069, PF00312
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS11
Chain IDs:EA (auth: BO)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS19
Chain IDs:J (auth: BP)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS9
Chain IDs:K (auth: BQ)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS17
Gene (Uniprot):RPS17
Chain IDs:L (auth: BR)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TU13 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS13
Gene (Uniprot):RPS18
Chain IDs:M (auth: BS)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TPG3 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS19
Chain IDs:N (auth: BT)
Chain Length:143
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS10
Chain IDs:O (auth: BU)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS21
Chain IDs:FA (auth: BV)
Chain Length:81
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:GA (auth: BW)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TG89 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:HA (auth: BX)
Chain Length:12
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SZ47 Pfam ID:PF00164
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS24
Chain IDs:IA (auth: BY)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS25
Gene (Uniprot):RPS25
Chain IDs:P (auth: BZ)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TDB3 Pfam ID:PF03297
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS26
Chain IDs:JA (auth: Ba)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS27
Chain IDs:KA (auth: Bb)
Chain Length:212
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:Q (auth: Bc)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1TIB4 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS14
Gene (Uniprot):RPS29
Chain IDs:R (auth: Bd)
Chain Length:220
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1U7M4 Pfam ID:PF00253
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS30
Chain IDs:LA (auth: Be)
Chain Length:257
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:S (auth: Bf)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SK22 Pfam ID:PF00240, PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein RACK 1
Gene (Uniprot):RACK1
Chain IDs:T (auth: Bg)
Chain Length:232
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
UniProt ID:G1SJB4 Pfam ID:PF00400
Polymer Type:polyribonucleotide
Molecule:ap/P-site tRNA
Chain IDs:B (auth: Bv)
Chain Length:81
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:pe/E-site-tRNA
Chain IDs:D (auth: Bw)
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:C (auth: Bx)
Chain Length:12
Number of Molecules:1
Biological Source:Enterobacteria phage SP6
Polymer Type:polypeptide(L)
Molecule:eukaryotic elongation factor 2 (eEF2)
Chain IDs:HC (auth: Ct)
Chain Length:853
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Ligand Molecules
GNP
MG
ZN
Primary Citation
tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Cell Rep 25 2676 2688.e7 (2018)
PMID: 30517857 DOI: 10.1016/j.celrep.2018.11.040

Abstact

Translocation moves the tRNA2⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA2⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6GZ3