› 6ybd

Electron Microscopy
3.3Å resolution

Structure of a human 48S translational initiation complex - eIF3

Released:
DOI: 10.2210/pdb6ybd/pdb
PDB entry 6ybd coloured by chain, front view.
PDB entry 6ybd coloured by chain, side view.
PDB entry 6ybd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of a human 48S translational initiation complex.
Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V
Science 369 1220-1227 (2020)
PMID: 32883864
Related structures: EMD-10769

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-126238 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
Eukaryotic translation initiation factor 3 subunit M Chain: 6
Molecule details ›
Chain: 6
Length: 374 amino acids
Theoretical weight: 42.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q7L2H7 (Residues: 1-374; Coverage: 100%)
Gene names: EIF3M, GA17, HFLB5, PCID1, PNAS-125
Sequence domains:
Eukaryotic translation initiation factor 3 subunit F Chain: 4
Molecule details ›
Chain: 4
Length: 357 amino acids
Theoretical weight: 37.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00303 (Residues: 1-357; Coverage: 100%)
Gene names: EIF3F, EIF3S5
Sequence domains:
Eukaryotic translation initiation factor 3 subunit A Chain: u
Molecule details ›
Chain: u
Length: 1382 amino acids
Theoretical weight: 166.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14152 (Residues: 1-1382; Coverage: 100%)
Gene names: EIF3A, EIF3S10, KIAA0139
Sequence domains: PCI domain
Eukaryotic translation initiation factor 3 subunit E Chain: v
Molecule details ›
Chain: v
Length: 445 amino acids
Theoretical weight: 52.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60228 (Residues: 1-445; Coverage: 100%)
Gene names: EIF3E, EIF3S6, INT6
Sequence domains:
Eukaryotic translation initiation factor 3 subunit C Chain: y
Molecule details ›
Chain: y
Length: 913 amino acids
Theoretical weight: 105.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99613 (Residues: 1-913; Coverage: 100%)
Gene names: EIF3C, EIF3S8
Sequence domains:
Eukaryotic translation initiation factor 3 subunit H Chain: 8
Molecule details ›
Chain: 8
Length: 352 amino acids
Theoretical weight: 39.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15372 (Residues: 1-352; Coverage: 100%)
Gene names: EIF3H, EIF3S3
Sequence domains:
Small ribosomal subunit protein eS7 Chain: G
Molecule details ›
Chain: G
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62081 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS27 Chain: H
Molecule details ›
Chain: H
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42677 (Residues: 1-84; Coverage: 100%)
Gene names: MPS1, RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS21 Chain: K
Molecule details ›
Chain: K
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63220 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein eS17 Chain: M
Molecule details ›
Chain: M
Length: 135 amino acids
Theoretical weight: 15.58 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08708 (Residues: 1-135; Coverage: 100%)
Gene names: RPS17, RPS17L
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS5 Chain: L
Molecule details ›
Chain: L
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P15880 (Residues: 1-293; Coverage: 100%)
Gene names: RPS2, RPS4
Sequence domains:
Small ribosomal subunit protein eS1 Chain: O
Molecule details ›
Chain: O
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61247 (Residues: 1-264; Coverage: 100%)
Gene names: FTE1, MFTL, RPS3A
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS2 Chain: N
Molecule details ›
Chain: N
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08865 (Residues: 1-295; Coverage: 100%)
Gene names: LAMBR, LAMR1, RPSA
Sequence domains:
Small ribosomal subunit protein eS26 Chain: Q
Molecule details ›
Chain: Q
Length: 115 amino acids
Theoretical weight: 13.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62854 (Residues: 1-115; Coverage: 100%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein uS11 Chain: P
Molecule details ›
Chain: P
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62263 (Residues: 1-151; Coverage: 100%)
Gene names: PRO2640, RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS15 Chain: I
Molecule details ›
Chain: I
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62277 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Sequence domains:
Eukaryotic translation initiation factor 3 subunit D Chain: x
Molecule details ›
Chain: x
Length: 548 amino acids
Theoretical weight: 64.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15371 (Residues: 1-548; Coverage: 100%)
Gene names: EIF3D, EIF3S7
Sequence domains: Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)
Eukaryotic translation initiation factor 3 subunit K Chain: 3
Molecule details ›
Chain: 3
Length: 218 amino acids
Theoretical weight: 25.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UBQ5 (Residues: 1-218; Coverage: 100%)
Gene names: ARG134, EIF3K, EIF3S12, HSPC029, MSTP001, PTD001
Sequence domains: CSN8/PSMD8/EIF3K family
Eukaryotic translation initiation factor 3 subunit L Chain: 5
Molecule details ›
Chain: 5
Length: 564 amino acids
Theoretical weight: 66.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y262 (Residues: 1-564; Coverage: 100%)
Gene names: EIF3EIP, EIF3L, EIF3S6IP, HSPC021, HSPC025, MSTP005
Sequence domains: RNA polymerase I-associated factor PAF67

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-10769

Quick links

Citations

12 review citations

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
11 more

2 mentions without citation

Structure of a human 48S translational initiation complex.
Brito Querido et al. (2020)
1 more