› 5k0y

Electron Microscopy
5.8Å resolution

m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face

Released:
DOI: 10.2210/pdb5k0y/pdb
PDB entry 5k0y coloured by chain, front view.
PDB entry 5k0y coloured by chain, side view.
PDB entry 5k0y coloured by chain, top view.
Source organisms:
Primary publication:
eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.
Simonetti A, Brito Querido J, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem Y
Mol Cell 63 206-217 (2016)
PMID: 27373335
Related structures: EMD-8190

Function and Biology Details

Reactions catalysed: 
GTP + H(2)O = GDP + phosphate
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 42-mer (preferred)
PDBe Complex ID:
PDB-CPX-239318 (preferred)
Entry contents:
39 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (42 distinct):
Eukaryotic translation initiation factor 2 subunit 1 Chain: P
Molecule details ›
Chain: P
Length: 266 amino acids
Theoretical weight: 30.63 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T2G4 (Residues: 6-271; Coverage: 94%)
Gene name: EIF2S1
Sequence domains:
Small ribosomal subunit protein uS17 Chain: G
Molecule details ›
Chain: G
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TRM4 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein uS9 Chain: H
Molecule details ›
Chain: H
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 32-172; Coverage: 82%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS4 Chain: I
Molecule details ›
Chain: I
Length: 263 amino acids
Theoretical weight: 29.66 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TK17 (Residues: 1-263; Coverage: 100%)
Gene name: RPS4X
Sequence domains:
Small ribosomal subunit protein uS14 Chain: J
Molecule details ›
Chain: J
Length: 53 amino acids
Theoretical weight: 6.36 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 4-56; Coverage: 95%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS4 Chain: K
Molecule details ›
Chain: K
Length: 182 amino acids
Theoretical weight: 21.27 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 7-188; Coverage: 94%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein uS13 Chain: L
Molecule details ›
Chain: L
Length: 137 amino acids
Theoretical weight: 16.17 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 6-142; Coverage: 90%)
Gene name: RPS18
Sequence domains: Ribosomal protein S13/S18
Eukaryotic translation initiation factor 3 subunit G Chain: M
Molecule details ›
Chain: M
Length: 38 amino acids
Theoretical weight: 4.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75821 (Residues: 103-140; Coverage: 12%)
Gene names: EIF3G, EIF3S4
Sequence domains: Eukaryotic translation initiation factor 3 subunit G
Eukaryotic translation initiation factor 3 subunit G Chain: O
Molecule details ›
Chain: O
Length: 77 amino acids
Theoretical weight: 8.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75821 (Residues: 239-315; Coverage: 24%)
Gene names: EIF3G, EIF3S4
Sequence domains: RNA recognition motif
Small ribosomal subunit protein uS12 Chain: Q
Molecule details ›
Chain: Q
Length: 142 amino acids
Theoretical weight: 15.76 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS19 Chain: R
Molecule details ›
Chain: R
Length: 141 amino acids
Theoretical weight: 15.81 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 4-144; Coverage: 97%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
protein-synthesizing GTPase Chain: S
Molecule details ›
Chain: S
Length: 422 amino acids
Theoretical weight: 45.86 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SRA8 (Residues: 52-479; Coverage: 86%)
Gene name: EIF2S3
Sequence domains:
Eukaryotic translation initiation factor 3 subunit I Chain: T
Molecule details ›
Chain: T
Length: 329 amino acids
Theoretical weight: 37.04 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: Q5IH81 (Residues: 1-329; Coverage: 99%)
Gene names: EIF3I, EIF3S2
Sequence domains:
Small ribosomal subunit protein uS7 Chain: U
Molecule details ›
Chain: U
Length: 191 amino acids
Theoretical weight: 21.53 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: U3KMN4 (Residues: 29-219; Coverage: 87%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS30 Chain: V
Molecule details ›
Chain: V
Length: 59 amino acids
Theoretical weight: 6.74 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein eS25 Chain: W
Molecule details ›
Chain: W
Length: 75 amino acids
Theoretical weight: 8.53 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 40-114; Coverage: 61%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS7 Chain: X
Molecule details ›
Chain: X
Length: 190 amino acids
Theoretical weight: 21.72 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 243-432; Coverage: 44%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS27 Chain: Y
Molecule details ›
Chain: Y
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TZ76 (Residues: 1-84; Coverage: 100%)
Gene name: RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein uS15 Chain: Z
Molecule details ›
Chain: Z
Length: 150 amino acids
Theoretical weight: 17.13 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 11-152; Coverage: 92%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS8 Chain: a
Molecule details ›
Chain: a
Length: 129 amino acids
Theoretical weight: 14.73 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TG89 (Residues: 2-130; Coverage: 99%)
Gene name: RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein eS21 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM82 (Residues: 24-80; Coverage: 51%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
ribosomal protein uS5 Chain: c
Molecule details ›
Chain: c
Length: 226 amino acids
Theoretical weight: 24.81 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
Translation initiation factor 2 subunit beta Chain: d
Molecule details ›
Chain: d
Length: 17 amino acids
Theoretical weight: 2.1 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: Q97W59 (Residues: 3-19; Coverage: 12%)
Gene names: SSO2381, aif2b, eif2b
Small ribosomal subunit protein eS17 Chain: e
Molecule details ›
Chain: e
Length: 126 amino acids
Theoretical weight: 14.58 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 1-126; Coverage: 93%)
Gene name: RPS17
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS2 Chain: f
Molecule details ›
Chain: f
Length: 208 amino acids
Theoretical weight: 23.36 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 2-209; Coverage: 71%)
Gene name: RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: g
Molecule details ›
Chain: g
Length: 227 amino acids
Theoretical weight: 25.16 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 39-265; Coverage: 81%)
Gene name: RPS3
Sequence domains:
Small ribosomal subunit protein uS10 Chain: h
Molecule details ›
Chain: h
Length: 104 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIZ2 (Residues: 16-119; Coverage: 87%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS1 Chain: i
Molecule details ›
Chain: i
Length: 215 amino acids
Theoretical weight: 24.94 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN72 (Residues: 19-233; Coverage: 81%)
Gene name: RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS11 Chain: j
Molecule details ›
Chain: j
Length: 136 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T1F0 (Residues: 16-151; Coverage: 90%)
Gene name: RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein eS26 Chain: k
Molecule details ›
Chain: k
Length: 99 amino acids
Theoretical weight: 11.32 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE8 (Residues: 2-100; Coverage: 86%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS28 Chain: l
Molecule details ›
Chain: l
Length: 64 amino acids
Theoretical weight: 7.26 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 5-68; Coverage: 93%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein RACK1 Chain: m
Molecule details ›
Chain: m
Length: 313 amino acids
Theoretical weight: 34.67 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 117-421; Coverage: 72%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein uS19 Chain: n
Molecule details ›
Chain: n
Length: 127 amino acids
Theoretical weight: 15.15 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U0Q2 (Residues: 4-130; Coverage: 88%)
Gene name: RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS8 Chain: o
Molecule details ›
Chain: o
Length: 206 amino acids
Theoretical weight: 23.9 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TJW1 (Residues: 2-207; Coverage: 99%)
Gene name: RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein eS31 Chain: p
Molecule details ›
Chain: p
Length: 71 amino acids
Theoretical weight: 8.36 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 114-184; Coverage: 38%)
Gene name: RPS27A
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein eS6 Chain: q
Molecule details ›
Chain: q
Length: 237 amino acids
Theoretical weight: 27.47 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM55 (Residues: 11-211; Coverage: 81%)
Gene name: RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS12 Chain: r
Molecule details ›
Chain: r
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 9-132; Coverage: 94%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
40S ribosomal protein S24 Chain: s
Molecule details ›
Chain: s
Length: 131 amino acids
Theoretical weight: 15.19 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TS40 (Residues: 3-133; Coverage: 99%)
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS10 Chain: t
Molecule details ›
Chain: t
Length: 98 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T168 (Residues: 61-158; Coverage: 44%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
tRNA Chain: N
Molecule details ›
Chain: N
Length: 75 nucleotides
Theoretical weight: 24.23 KDa
Sequence domains: tRNA
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1776 nucleotides
Theoretical weight: 572.79 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Messenger RNA Chain: F
Molecule details ›
Chain: F
Length: 30 nucleotides
Theoretical weight: 9.6 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.8Å
Relevant EMDB volumes: EMD-8190
Expression systems:
  • Oryctolagus cuniculus
  • Homo sapiens

Quick links

Citations

19 review citations

Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation.
Hinnebusch AG. (2017)
18 more

6 mentions without citation

eIF2B conformation and assembly state regulate the integrated stress response.
Schoof et al. (2021)
5 more