› 6yan

Electron Microscopy
3.48Å resolution

Mammalian 48S late-stage translation initiation complex with histone 4 mRNA

Released:
DOI: 10.2210/pdb6yan/pdb
PDB entry 6yan coloured by chain, front view.
PDB entry 6yan coloured by chain, side view.
PDB entry 6yan coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y
Cell Rep 31 107497 (2020)
PMID: 32268096
Related structures: EMD-10762

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 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-239237 (preferred)
Entry contents:
36 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (39 distinct):
Small ribosomal subunit protein eS32 Chain: l
Molecule details ›
Chain: l
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A087WNH4 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Small ribosomal subunit protein uS2 Chain: C
Molecule details ›
Chain: C
Length: 208 amino acids
Theoretical weight: 23.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 2-209; Coverage: 71%)
Gene name: RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: D
Molecule details ›
Chain: D
Length: 215 amino acids
Theoretical weight: 24.94 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN72 (Residues: 19-233; Coverage: 81%)
Gene name: RPS3A
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 226 amino acids
Theoretical weight: 24.81 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS3 Chain: F
Molecule details ›
Chain: F
Length: 227 amino acids
Theoretical weight: 25.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 1-227; Coverage: 93%)
Gene name: RPS3
Sequence domains:
Small ribosomal subunit protein eS4 Chain: G
Molecule details ›
Chain: G
Length: 263 amino acids
Theoretical weight: 29.66 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TK17 (Residues: 1-263; Coverage: 100%)
Gene name: RPS4X
Sequence domains:
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
Chain: H
Length: 191 amino acids
Theoretical weight: 21.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFM5 (Residues: 14-204; Coverage: 94%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S6 Chain: I
Molecule details ›
Chain: I
Length: 237 amino acids
Theoretical weight: 27.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5K1UJS7 (Residues: 1-237; Coverage: 95%)
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: J
Molecule details ›
Chain: J
Length: 190 amino acids
Theoretical weight: 21.72 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 5-194; Coverage: 98%)
Gene name: RPS7
Small ribosomal subunit protein eS8 Chain: K
Molecule details ›
Chain: K
Length: 206 amino acids
Theoretical weight: 23.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TJW1 (Residues: 2-207; Coverage: 99%)
Gene name: RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: L
Molecule details ›
Chain: L
Length: 182 amino acids
Theoretical weight: 21.27 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 7-188; Coverage: 94%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein eS10 Chain: M
Molecule details ›
Chain: M
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 uS17 Chain: N
Molecule details ›
Chain: N
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TRM4 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Sequence domains:
Small ribosomal subunit protein eS12 Chain: O
Molecule details ›
Chain: O
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 9-132; Coverage: 94%)
Gene name: RPS12
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chain: P
Molecule details ›
Chain: P
Length: 150 amino acids
Theoretical weight: 17.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 2-151; Coverage: 99%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chain: Q
Molecule details ›
Chain: Q
Length: 136 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T1F0 (Residues: 16-151; Coverage: 90%)
Gene name: RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS9 Chain: S
Molecule details ›
Chain: S
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 6-146; Coverage: 97%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: T
Molecule details ›
Chain: T
Length: 126 amino acids
Theoretical weight: 14.58 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 1-126; Coverage: 93%)
Gene name: RPS17
Sequence domains: Ribosomal S17
Small ribosomal subunit protein eS19 Chain: V
Molecule details ›
Chain: V
Length: 141 amino acids
Theoretical weight: 15.81 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 4-144; Coverage: 97%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: W
Molecule details ›
Chain: W
Length: 104 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIZ2 (Residues: 16-119; Coverage: 87%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21 Chain: X
Molecule details ›
Chain: X
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM82 (Residues: 1-82; Coverage: 99%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8 Chain: Y
Molecule details ›
Chain: Y
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: Z
Molecule details ›
Chain: Z
Length: 142 amino acids
Theoretical weight: 15.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: a
Molecule details ›
Chain: a
Length: 126 amino acids
Theoretical weight: 14.58 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TS40 (Residues: 3-128; Coverage: 95%)
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS26 Chain: b
Molecule details ›
Chain: b
Length: 99 amino acids
Theoretical weight: 11.32 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE8 (Residues: 2-100; Coverage: 86%)
Gene name: RPS26
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS27 Chain: c
Molecule details ›
Chain: c
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TZ76 (Residues: 1-84; Coverage: 100%)
Gene name: RPS27
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28 Chain: d
Molecule details ›
Chain: d
Length: 64 amino acids
Theoretical weight: 7.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 5-68; Coverage: 93%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: e
Molecule details ›
Chain: e
Length: 53 amino acids
Theoretical weight: 6.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 4-56; Coverage: 95%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: f
Molecule details ›
Chain: f
Length: 71 amino acids
Theoretical weight: 8.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 82-152; Coverage: 46%)
Gene name: RPS27A
Sequence domains:
Small ribosomal subunit protein RACK1 Chain: g
Molecule details ›
Chain: g
Length: 313 amino acids
Theoretical weight: 34.67 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 2-314; Coverage: 99%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein eS25 Chain: h
Molecule details ›
Chain: h
Length: 75 amino acids
Theoretical weight: 8.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 40-114; Coverage: 61%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS30 Chain: i
Molecule details ›
Chain: i
Length: 59 amino acids
Theoretical weight: 6.74 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Eukaryotic translation initiation factor 2 subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 30.63 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T2G4 (Residues: 6-271; Coverage: 94%)
Gene name: EIF2S1
Sequence domains:
eukaryotic translation initiation factor 2 subunit gamma Chain: B
Molecule details ›
Chain: B
Length: 422 amino acids
Theoretical weight: 45.86 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS13 Chain: U
Molecule details ›
Chain: U
Length: 142 amino acids
Theoretical weight: 16.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 6-147; Coverage: 93%)
Gene name: RPS18
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS19 Chain: R
Molecule details ›
Chain: R
Length: 135 amino acids
Theoretical weight: 15.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U0Q2 (Residues: 4-138; Coverage: 93%)
Gene name: RPS15
Sequence domains: Ribosomal protein S19
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1863 nucleotides
Theoretical weight: 601.02 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
histone 4 (H4) mRNA Chain: 3
Molecule details ›
Chain: 3
Length: 36 nucleotides
Theoretical weight: 11.69 KDa
initiator methionylated tRNA Chain: 1
Molecule details ›
Chain: 1
Length: 75 nucleotides
Theoretical weight: 24.38 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
1 modified residue:
Ligand T6A 1 x T6A

Experiments and Validation Details

Entry percentile scores
Resolution: 3.48Å
Relevant EMDB volumes: EMD-10762

Quick links

Citations

7 review citations

The Structural Dynamics of Translation.
Korostelev AA. (2022)
6 more

1 mention without citation

Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Simonetti et al. (2020)