› 6gz3

Electron Microscopy
3.6Å resolution

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)

Released:
DOI: 10.2210/pdb6gz3/pdb
PDB entry 6gz3 coloured by chain, front view.
PDB entry 6gz3 coloured by chain, side view.
PDB entry 6gz3 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV
Cell Rep 25 2676-2688.e7 (2018)
PMID: 30517857
Related structures: EMD-0098

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 86-mer (preferred)
PDBe Complex ID:
PDB-CPX-110575 (preferred)
Entry contents:
79 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (86 distinct):
ribosomal protein uS3 Chain: BD
Molecule details ›
Chain: BD
Length: 220 amino acids
Theoretical weight: 24.36 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS7 Chain: BF
Molecule details ›
Chain: BF
Length: 190 amino acids
Theoretical weight: 21.42 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFM5 (Residues: 15-204; Coverage: 93%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS10 Chain: BK
Molecule details ›
Chain: BK
Length: 98 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPV3 (Residues: 1-98; Coverage: 59%)
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein eS12 Chain: BM
Molecule details ›
Chain: BM
Length: 120 amino acids
Theoretical weight: 13.39 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 11-130; Coverage: 91%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
ribosomal protein uS19 Chain: BP
Molecule details ›
Chain: BP
Length: 120 amino acids
Theoretical weight: 14.27 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uS9 Chain: BQ
Molecule details ›
Chain: BQ
Length: 139 amino acids
Theoretical weight: 15.77 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein eS17 Chain: BR
Molecule details ›
Chain: BR
Length: 125 amino acids
Theoretical weight: 14.45 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 2-126; Coverage: 93%)
Gene name: RPS17
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13 Chain: BS
Molecule details ›
Chain: BS
Length: 139 amino acids
Theoretical weight: 16.38 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 4-142; Coverage: 91%)
Gene name: RPS18
Sequence domains: Ribosomal protein S13/S18
ribosomal protein eS19 Chain: BT
Molecule details ›
Chain: BT
Length: 143 amino acids
Theoretical weight: 15.82 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uS10 Chain: BU
Molecule details ›
Chain: BU
Length: 97 amino acids
Theoretical weight: 11.03 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein eS25 Chain: BZ
Molecule details ›
Chain: BZ
Length: 86 amino acids
Theoretical weight: 9.8 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 27-112; Coverage: 69%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS28 Chain: Bc
Molecule details ›
Chain: Bc
Length: 62 amino acids
Theoretical weight: 7.01 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 7-68; Coverage: 90%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: Bd
Molecule details ›
Chain: Bd
Length: 51 amino acids
Theoretical weight: 6.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 5-55; Coverage: 91%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: Bf
Molecule details ›
Chain: Bf
Length: 73 amino acids
Theoretical weight: 8.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 111-183; Coverage: 39%)
Gene name: RPS27A
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chain: Bg
Molecule details ›
Chain: Bg
Length: 314 amino acids
Theoretical weight: 34.73 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 117-422; Coverage: 72%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
ribosomal protein uS2 Chain: BA
Molecule details ›
Chain: BA
Length: 215 amino acids
Theoretical weight: 24.25 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein eS1 Chain: BB
Molecule details ›
Chain: BB
Length: 212 amino acids
Theoretical weight: 24.66 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SS70 (Residues: 22-233; Coverage: 80%)
Gene name: RPS3A
Sequence domains: Ribosomal S3Ae family
ribosomal protein uS5 Chain: BC
Molecule details ›
Chain: BC
Length: 222 amino acids
Theoretical weight: 24.57 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eS4 Chain: BE
Molecule details ›
Chain: BE
Length: 257 amino acids
Theoretical weight: 28.89 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein eS6 Chain: BG
Molecule details ›
Chain: BG
Length: 232 amino acids
Theoretical weight: 26.91 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM55 (Residues: 11-211; Coverage: 81%)
Gene name: RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: BH
Molecule details ›
Chain: BH
Length: 183 amino acids
Theoretical weight: 20.99 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 250-432; Coverage: 42%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
ribosomal protein eS8 Chain: BI
Molecule details ›
Chain: BI
Length: 207 amino acids
Theoretical weight: 24.13 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS4 Chain: BJ
Molecule details ›
Chain: BJ
Length: 179 amino acids
Theoretical weight: 21.22 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 2-180; Coverage: 92%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS17 Chain: BL
Molecule details ›
Chain: BL
Length: 153 amino acids
Theoretical weight: 17.91 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TRM4 (Residues: 6-158; Coverage: 97%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS15 Chain: BN
Molecule details ›
Chain: BN
Length: 149 amino acids
Theoretical weight: 17.06 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 11-151; Coverage: 91%)
Gene name: RPS13
Sequence domains:
ribosomal protein uS11 Chain: BO
Molecule details ›
Chain: BO
Length: 136 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eS21 Chain: BV
Molecule details ›
Chain: BV
Length: 81 amino acids
Theoretical weight: 8.86 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS8 Chain: BW
Molecule details ›
Chain: BW
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TG89 (Residues: 2-130; Coverage: 99%)
Gene name: RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: BX
Molecule details ›
Chain: BX
Length: 141 amino acids
Theoretical weight: 15.63 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 2-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
ribosomal protein eS24 Chain: BY
Molecule details ›
Chain: BY
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eS26 Chain: Ba
Molecule details ›
Chain: Ba
Length: 97 amino acids
Theoretical weight: 11.09 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eS27 Chain: Bb
Molecule details ›
Chain: Bb
Length: 80 amino acids
Theoretical weight: 9 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eS30 Chain: Be
Molecule details ›
Chain: Be
Length: 55 amino acids
Theoretical weight: 6.24 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL2 Chain: AA
Molecule details ›
Chain: AA
Length: 252 amino acids
Theoretical weight: 27.46 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TT27 (Residues: 2-217; Coverage: 85%)
Gene name: RPL8
Sequence domains:
ribosomal protein uL3 Chain: AB
Molecule details ›
Chain: AB
Length: 394 amino acids
Theoretical weight: 45.22 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL4 Chain: AC
Molecule details ›
Chain: AC
Length: 363 amino acids
Theoretical weight: 41.17 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL18 Chain: AD
Molecule details ›
Chain: AD
Length: 294 amino acids
Theoretical weight: 34.09 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL6 Chain: AE
Molecule details ›
Chain: AE
Length: 194 amino acids
Theoretical weight: 22.26 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL30 Chain: AF
Molecule details ›
Chain: AF
Length: 234 amino acids
Theoretical weight: 27.73 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL8 Chain: AG
Molecule details ›
Chain: AG
Length: 234 amino acids
Theoretical weight: 26.72 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL6 Chain: AH
Molecule details ›
Chain: AH
Length: 191 amino acids
Theoretical weight: 21.77 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL16 Chain: AI
Molecule details ›
Chain: AI
Length: 211 amino acids
Theoretical weight: 24.38 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZQ2 (Residues: 3-213; Coverage: 99%)
Gene name: RPL10
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5 Chain: AJ
Molecule details ›
Chain: AJ
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUB8 (Residues: 9-177; Coverage: 95%)
Gene name: RPL11
Sequence domains:
ribosomal protein eL13 Chain: AL
Molecule details ›
Chain: AL
Length: 205 amino acids
Theoretical weight: 23.57 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL14 Chain: AM
Molecule details ›
Chain: AM
Length: 139 amino acids
Theoretical weight: 16.22 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL15 Chain: AN
Molecule details ›
Chain: AN
Length: 203 amino acids
Theoretical weight: 24.08 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T0C1 (Residues: 2-204; Coverage: 100%)
Gene name: RPL15
Sequence domains: Ribosomal L15
ribosomal protein uL13 Chain: AO
Molecule details ›
Chain: AO
Length: 195 amino acids
Theoretical weight: 22.82 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL22 Chain: AP
Molecule details ›
Chain: AP
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL18 Chain: AQ
Molecule details ›
Chain: AQ
Length: 187 amino acids
Theoretical weight: 21.56 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL19 Chain: AR
Molecule details ›
Chain: AR
Length: 181 amino acids
Theoretical weight: 21.74 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL20 Chain: AS
Molecule details ›
Chain: AS
Length: 175 amino acids
Theoretical weight: 20.66 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL21 Chain: AT
Molecule details ›
Chain: AT
Length: 157 amino acids
Theoretical weight: 18.28 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHQ2 (Residues: 2-158; Coverage: 98%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
ribosomal protein eL22 Chain: AU
Molecule details ›
Chain: AU
Length: 99 amino acids
Theoretical weight: 11.48 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL14 Chain: AV
Molecule details ›
Chain: AV
Length: 129 amino acids
Theoretical weight: 13.83 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T6D1 (Residues: 12-140; Coverage: 92%)
Gene name: RPL23
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24 Chain: AW
Molecule details ›
Chain: AW
Length: 121 amino acids
Theoretical weight: 14.09 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SE28 (Residues: 2-122; Coverage: 77%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
ribosomal protein uL23 Chain: AX
Molecule details ›
Chain: AX
Length: 117 amino acids
Theoretical weight: 13.61 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL24 Chain: AY
Molecule details ›
Chain: AY
Length: 127 amino acids
Theoretical weight: 15.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SQH0 (Residues: 1-127; Coverage: 88%)
Gene name: RPL26
Sequence domains:
Large ribosomal subunit protein eL27 Chain: AZ
Molecule details ›
Chain: AZ
Length: 134 amino acids
Theoretical weight: 15.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TXF6 (Residues: 3-136; Coverage: 99%)
Gene name: RPL27
Sequence domains:
ribosomal protein uL15 Chain: Aa
Molecule details ›
Chain: Aa
Length: 147 amino acids
Theoretical weight: 16.47 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL29 Chain: Ab
Molecule details ›
Chain: Ab
Length: 68 amino acids
Theoretical weight: 8 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL30 Chain: Ac
Molecule details ›
Chain: Ac
Length: 103 amino acids
Theoretical weight: 11.5 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL31 Chain: Ad
Molecule details ›
Chain: Ad
Length: 106 amino acids
Theoretical weight: 12.51 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHG0 (Residues: 18-123; Coverage: 85%)
Gene name: RPL31
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: Ae
Molecule details ›
Chain: Ae
Length: 129 amino acids
Theoretical weight: 15.18 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUN8 (Residues: 24-152; Coverage: 82%)
Gene name: RPL32
Sequence domains: Ribosomal protein L32
ribosomal protein eL33 Chain: Af
Molecule details ›
Chain: Af
Length: 109 amino acids
Theoretical weight: 12.43 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL34 Chain: Ag
Molecule details ›
Chain: Ag
Length: 114 amino acids
Theoretical weight: 12.99 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein uL29 Chain: Ah
Molecule details ›
Chain: Ah
Length: 122 amino acids
Theoretical weight: 14.46 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL36 Chain: Ai
Molecule details ›
Chain: Ai
Length: 97 amino acids
Theoretical weight: 11.37 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL37 Chain: Aj
Molecule details ›
Chain: Aj
Length: 84 amino acids
Theoretical weight: 9.86 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: U3KPD5 (Residues: 2-85; Coverage: 87%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
ribosomal protein eL38 Chain: Ak
Molecule details ›
Chain: Ak
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL39 Chain: Al
Molecule details ›
Chain: Al
Length: 50 amino acids
Theoretical weight: 6.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SYU7 (Residues: 2-51; Coverage: 98%)
Gene name: RPL39
Sequence domains: Ribosomal L39 protein
ribosomal protein eL40 Chain: Am
Molecule details ›
Chain: Am
Length: 50 amino acids
Theoretical weight: 5.96 KDa
Source organism: Oryctolagus cuniculus
ribosomal protein eL41 Chain: An
Molecule details ›
Chain: An
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL42 Chain: Ao
Molecule details ›
Chain: Ao
Length: 105 amino acids
Theoretical weight: 12.35 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T040 (Residues: 2-100; Coverage: 89%)
Gene name: RPL36A
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43 Chain: Ap
Molecule details ›
Chain: Ap
Length: 91 amino acids
Theoretical weight: 10.17 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SY53 (Residues: 2-92; Coverage: 99%)
Gene name: RPL37A
Sequence domains: Ribosomal L37ae protein family
ribosomal protein eL28 Chain: At
Molecule details ›
Chain: At
Length: 122 amino acids
Theoretical weight: 13.99 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL1 Chain: Au
Molecule details ›
Chain: Au
Length: 217 amino acids
Theoretical weight: 24.88 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SKZ8 (Residues: 1-217; Coverage: 100%)
Gene name: RPL10A
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL11 Chain: Aq
Molecule details ›
Chain: Aq
Length: 151 amino acids
Theoretical weight: 16.29 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SMR7 (Residues: 13-163; Coverage: 92%)
Gene name: RPL12
Sequence domains:
ribosomal protein uL10 Chain: AK
Molecule details ›
Chain: AK
Length: 202 amino acids
Theoretical weight: 22.22 KDa
Source organism: Oryctolagus cuniculus
eukaryotic elongation factor 2 (eEF2) Chain: Ct
Molecule details ›
Chain: Ct
Length: 853 amino acids
Theoretical weight: 95.06 KDa
Source organism: Oryctolagus cuniculus
28S ribosomal RNA Chain: A2
Molecule details ›
Chain: A2
Length: 3612 nucleotides
Theoretical weight: 1170.16 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
ap/P-site tRNA Chain: Bv
Molecule details ›
Chain: Bv
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA
Messenger RNA Chain: Bx
Molecule details ›
Chain: Bx
Length: 12 nucleotides
Theoretical weight: 3.84 KDa
pe/E-site-tRNA Chain: Bw
Molecule details ›
Chain: Bw
Length: 76 nucleotides
Theoretical weight: 24.53 KDa
Sequence domains: tRNA
18S Ribosomal RNA Chain: B1
Molecule details ›
Chain: B1
Length: 1708 nucleotides
Theoretical weight: 551.11 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
5.8S ribosomal RNA Chain: A3
Molecule details ›
Chain: A3
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chain: A4
Molecule details ›
Chain: A4
Length: 119 nucleotides
Theoretical weight: 38.39 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 327 x MG
Ligand ZN 5 x ZN
Ligand GNP 1 x GNP
1 modified residue:
Ligand DDE 1 x DDE

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-0098

Quick links

Citations

4 review citations

Approaches for measuring the dynamics of RNA-protein interactions.
Licatalosi et al. (2020)
3 more

6 mentions without citation

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Flis et al. (2018)
5 more