ISDA

Deposition Date 2018-07-03

Release Date 2018-12-05

Last Version Date 2022-03-30

Entry Detail

PDB ID:

6GZ5

Keywords:

RIBOSOME

Title:

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)

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:

3.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download 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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL2
Chain IDs:OA (auth: AA)
Chain Length:147
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL3
Chain IDs:PA (auth: AB)
Chain Length:68
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:294
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL6
Chain IDs:SA (auth: AE)
Chain Length:194
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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL16
Chain IDs:WA (auth: AI)
Chain Length:97
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL5
Chain IDs:XA (auth: AJ)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL10
Chain IDs:GC (auth: AK)
Chain Length:202
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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL15
Chain IDs:AB (auth: AN)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL13
Chain IDs:BB (auth: AO)
Chain Length:105
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL22
Chain IDs:CB (auth: AP)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL18
Chain IDs:DB (auth: AQ)
Chain Length:151
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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL21
Chain IDs:GB (auth: AT)
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL22
Chain IDs:HB (auth: AU)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL14
Chain IDs:IB (auth: AV)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL24
Chain IDs:JB (auth: AW)
Chain Length:121
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL23
Chain IDs:KB (auth: AX)
Chain Length:117
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL24
Chain IDs:LB (auth: AY)
Chain Length:127
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL27
Chain IDs:MB (auth: AZ)
Chain Length:134
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL15
Chain IDs:NB (auth: Aa)
Chain Length:147
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL29
Chain IDs:OB (auth: Ab)
Chain Length:68
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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL31
Chain IDs:QB (auth: Ad)
Chain Length:294
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL32
Chain IDs:RB (auth: Ae)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL37
Chain IDs:WB (auth: Aj)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL38
Chain IDs:XB (auth: Ak)
Chain Length:202
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL39
Chain IDs:YB (auth: Al)
Chain Length:50
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL42
Chain IDs:BC (auth: Ao)
Chain Length:105
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL43
Chain IDs:CC (auth: Ap)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL11
Chain IDs:FC (auth: Aq)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL28
Chain IDs:DC (auth: At)
Chain Length:122
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL1
Chain IDs:EC (auth: Au)
Chain Length:99
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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:215
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS1
Chain IDs:V (auth: BB)
Chain Length:212
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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:55
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS7
Chain IDs:G (auth: BF)
Chain Length:73
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS6
Chain IDs:Y (auth: BG)
Chain Length:232
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS7
Chain IDs:Z (auth: BH)
Chain Length:183
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS8
Chain IDs:AA (auth: BI)
Chain Length:207
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS4
Chain IDs:BA (auth: BJ)
Chain Length:179
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS10
Chain IDs:H (auth: BK)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS17
Chain IDs:CA (auth: BL)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS12
Chain IDs:I (auth: BM)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS15
Chain IDs:DA (auth: BN)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS17
Chain IDs:L (auth: BR)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS13
Chain IDs:M (auth: BS)
Chain Length:139
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS8
Chain IDs:GA (auth: BW)
Chain Length:76
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS12
Chain IDs:HA (auth: BX)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS24
Chain IDs:IA (auth: BY)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS25
Chain IDs:P (auth: BZ)
Chain Length:86
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS26
Chain IDs:JA (auth: Ba)
Chain Length:215
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

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS28
Chain IDs:Q (auth: Bc)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS14
Chain IDs:R (auth: Bd)
Chain Length:220
Number of Molecules:1
Biological Source:Enterobacteria phage SP6

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS30
Chain IDs:LA (auth: Be)
Chain Length:55
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS31
Chain IDs:S (auth: Bf)
Chain Length:73
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:ribosomal protein RACK 1
Chain IDs:T (auth: Bg)
Chain Length:232
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:P/P-site-tRNA
Chain IDs:B (auth: Bv)
Chain Length:81
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:E/E-site-tRNA
Chain IDs:D (auth: Bw)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:C (auth: Bx)
Chain Length:141
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

Primary Citation

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J, Holm, M, Rundlet, E.J, Loerke, J, Hilal, T, Dabrowski, M, Burger, J, Mielke, T, Blanchard, S.C, Spahn, C.M.T, Budkevich, T.V.Show

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