› 6ybs

Electron Microscopy
3.1Å resolution

Structure of a human 48S translational initiation complex - head

Released:
DOI: 10.2210/pdb6ybs/pdb
PDB entry 6ybs coloured by chain, front view.
PDB entry 6ybs coloured by chain, side view.
PDB entry 6ybs 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-10772

Function and Biology Details

Reaction catalysed: 
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 octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-127449 (preferred)
Entry contents:
17 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (18 distinct):
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)
Small ribosomal subunit protein RACK1 Chain: c
Molecule details ›
Chain: c
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63244 (Residues: 1-317; Coverage: 100%)
Gene names: GNB2L1, HLC7, PIG21, RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein eS28 Chain: n
Molecule details ›
Chain: n
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62857 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS17 Chain: X
Molecule details ›
Chain: X
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 uS10 Chain: h
Molecule details ›
Chain: h
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60866 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Eukaryotic translation initiation factor 3 subunit G Chain: o
Molecule details ›
Chain: o
Length: 320 amino acids
Theoretical weight: 35.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O75821 (Residues: 1-320; Coverage: 100%)
Gene names: EIF3G, EIF3S4
Sequence domains:
Small ribosomal subunit protein eS10 Chain: a
Molecule details ›
Chain: a
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46783 (Residues: 1-165; Coverage: 100%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein eS12 Chain: m
Molecule details ›
Chain: m
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25398 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS14 Chain: i
Molecule details ›
Chain: i
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62273 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS19 Chain: b
Molecule details ›
Chain: b
Length: 145 amino acids
Theoretical weight: 17.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62841 (Residues: 1-145; Coverage: 100%)
Gene names: RIG, RPS15
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS3 Chain: Z
Molecule details ›
Chain: Z
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P23396 (Residues: 1-243; Coverage: 100%)
Gene names: OK/SW-cl.26, RPS3
Sequence domains:
Small ribosomal subunit protein eS19 Chain: d
Molecule details ›
Chain: d
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39019 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein eS25 Chain: e
Molecule details ›
Chain: e
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62851 (Residues: 1-125; Coverage: 100%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein uS13 Chain: f
Molecule details ›
Chain: f
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62269 (Residues: 1-152; Coverage: 100%)
Gene names: D6S218E, RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS7 Chain: V
Molecule details ›
Chain: V
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46782 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Ubiquitin-ribosomal protein eS31 fusion protein Chain: k
Molecule details ›
Chain: k
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62979 (Residues: 1-156; Coverage: 100%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains:
Small ribosomal subunit protein uS9 Chain: Y
Molecule details ›
Chain: Y
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62249 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1869 nucleotides
Theoretical weight: 603.13 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 29 x MG
Ligand ZN 1 x ZN
11 modified residues:
Ligand A2M 7 x A2M
Ligand OMU 2 x OMU
Ligand PSU 6 x PSU
Ligand OMC 3 x OMC
Ligand OMG 3 x OMG
Ligand 5MU 1 x 5MU
Ligand JMH 1 x JMH
Ligand 5MC 1 x 5MC
Ligand UR3 1 x UR3
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10772

Quick links

Citations

12 review citations

Control of the eIF4E activity: structural insights and pharmacological implications.
Romagnoli et al. (2021)
11 more

2 mentions without citation

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