› 8p09

Electron Microscopy
3.3Å resolution

48S late-stage initiation complex with non methylated mRNA

Released:
DOI: 10.2210/pdb8p09/pdb
PDB entry 8p09 coloured by chain, front view.
PDB entry 8p09 coloured by chain, side view.
PDB entry 8p09 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
N6-methyladenosine in 5' UTR does not promote translation initiation.
Guca E, Alarcon R, Palo MZ, Santos L, Alonso-Gil S, Davyt M, de Lima LHF, Boissier F, Das S, Zagrovic B, Puglisi JD, Hashem Y, Ignatova Z
Mol Cell 84 584-595.e6 (2024)
PMID: 38244546
Related structures: EMD-17330

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 40-mer (preferred)
PDBe Complex ID:
PDB-CPX-275607 (preferred)
Entry contents:
37 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (40 distinct):
Eukaryotic translation initiation factor 2 subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 284 amino acids
Theoretical weight: 32.79 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T2G4 (Residues: 1-284; Coverage: 100%)
Gene name: EIF2S1
Sequence domains:
Small ribosomal subunit protein uS2 Chain: C
Molecule details ›
Chain: C
Length: 207 amino acids
Theoretical weight: 23.27 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 3-209; Coverage: 70%)
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 S2 Chain: E
Molecule details ›
Chain: E
Length: 270 amino acids
Theoretical weight: 29.1 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: U3KMN4 (Residues: 29-219; Coverage: 87%)
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: 27.48 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: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 1-194; Coverage: 100%)
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: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 1-132; Coverage: 100%)
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: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T1F0 (Residues: 1-151; Coverage: 100%)
Gene name: RPS14
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS19 Chain: R
Molecule details ›
Chain: R
Length: 145 amino acids
Theoretical weight: 17.05 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U0Q2 (Residues: 1-145; Coverage: 100%)
Gene name: RPS15
Sequence domains: Ribosomal protein S19
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: 135 amino acids
Theoretical weight: 15.55 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 1-135; Coverage: 100%)
Gene name: RPS17
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13 Chain: U
Molecule details ›
Chain: U
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 1-152; Coverage: 100%)
Gene name: RPS18
Sequence domains: Ribosomal protein S13/S18
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: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIZ2 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21 Chain: X
Molecule details ›
Chain: X
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: Q32PB8 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8 Chain: Y
Molecule details ›
Chain: Y
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TG89 (Residues: 1-130; Coverage: 100%)
Gene name: RPS15A
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: Z
Molecule details ›
Chain: Z
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24 Chain: a
Molecule details ›
Chain: a
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5F9D2E6 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS26 Chain: b
Molecule details ›
Chain: b
Length: 115 amino acids
Theoretical weight: 12.96 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE8 (Residues: 1-115; Coverage: 100%)
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: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: e
Molecule details ›
Chain: e
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 1-56; Coverage: 100%)
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
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein Chain: i
Molecule details ›
Chain: i
Length: 133 amino acids
Theoretical weight: 14.5 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 1-133; Coverage: 100%)
Gene name: FAU
Sequence domains:
Eukaryotic translation initiation factor 4C Chain: j
Molecule details ›
Chain: j
Length: 111 amino acids
Theoretical weight: 12.79 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SYS4 (Residues: 5-115; Coverage: 77%)
Sequence domains: Translation initiation factor 1A / IF-1
ATP binding cassette subfamily E member 1 Chain: k
Molecule details ›
Chain: k
Length: 595 amino acids
Theoretical weight: 66.99 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SG72 (Residues: 4-598; Coverage: 99%)
Sequence domains:
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 eS25 Chain: n
Molecule details ›
Chain: n
Length: 124 amino acids
Theoretical weight: 13.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 1-124; Coverage: 100%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
initiator methionylated tRNA Chain: 1
Molecule details ›
Chain: 1
Length: 75 nucleotides
Theoretical weight: 24.38 KDa
Sequence domains: tRNA
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1863 nucleotides
Theoretical weight: 601.02 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Messenger RNA Chain: 3
Molecule details ›
Chain: 3
Length: 9 nucleotides
Theoretical weight: 2.85 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 230 x MG
1 modified residue:
Ligand T6A 1 x T6A

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-17330

Quick links

Citations

1 review citation

Next generation sequencing technologies to address aberrant mRNA translation in cancer.
Román et al. (2024)
2 other articles