› 4d5l

Electron Microscopy
9Å resolution

Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state

Released:
DOI: 10.2210/pdb4d5l/pdb
PDB entry 4d5l coloured by chain, front view.
PDB entry 4d5l coloured by chain, side view.
PDB entry 4d5l coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES.
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CM
Mol Cell 57 422-32 (2015)
PMID: 25601755
Related structures: EMD-2810

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 34-mer (preferred)
PDBe Complex ID:
PDB-CPX-239319 (preferred)
Entry contents:
33 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (34 distinct):
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 32.88 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 1-295; Coverage: 100%)
Gene name: RPSA
Sequence domains:
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
Length: 264 amino acids
Theoretical weight: 30 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SS70 (Residues: 1-264; Coverage: 100%)
Gene name: RPS3A
Sequence domains: Ribosomal S3Ae family
Large ribosomal subunit protein uL30 Chain: C
Molecule details ›
Chain: C
Length: 293 amino acids
Theoretical weight: 31.38 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SV32 (Residues: 196-233; Coverage: 15%)
Gene name: RPL7
Small ribosomal subunit protein uS3 Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.73 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 39-281; Coverage: 87%)
Gene name: RPS3
Sequence domains:
Small ribosomal subunit protein eS4 Chain: E
Molecule details ›
Chain: E
Length: 263 amino acids
Theoretical weight: 29.51 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TK17 (Residues: 1-263; Coverage: 100%)
Gene name: RPS4X
Sequence domains:
Small ribosomal subunit protein uS7 Chain: F
Molecule details ›
Chain: F
Length: 204 amino acids
Theoretical weight: 22.91 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFM5 (Residues: 1-204; Coverage: 100%)
Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM55 (Residues: 11-211; Coverage: 81%)
Gene name: RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: H
Molecule details ›
Chain: H
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 239-432; Coverage: 45%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: I
Molecule details ›
Chain: I
Length: 208 amino acids
Theoretical weight: 24.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TJW1 (Residues: 1-208; Coverage: 100%)
Gene name: RPS8
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: J
Molecule details ›
Chain: J
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: K
Molecule details ›
Chain: K
Length: 165 amino acids
Theoretical weight: 18.93 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T168 (Residues: 61-225; Coverage: 73%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17 Chain: L
Molecule details ›
Chain: L
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: M
Molecule details ›
Chain: M
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: N
Molecule details ›
Chain: N
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 1-10, 11-152; Coverage: 99%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chain: O
Molecule details ›
Chain: O
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: P
Molecule details ›
Chain: P
Length: 145 amino acids
Theoretical weight: 17.08 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: Q
Molecule details ›
Chain: Q
Length: 146 amino acids
Theoretical weight: 16.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 27-172; Coverage: 85%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: R
Molecule details ›
Chain: R
Length: 135 amino acids
Theoretical weight: 15.58 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: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: U
Molecule details ›
Chain: U
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: V
Molecule details ›
Chain: V
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM82 (Residues: 24-80; Coverage: 51%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8 Chain: W
Molecule details ›
Chain: W
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: X
Molecule details ›
Chain: X
Length: 142 amino acids
Theoretical weight: 15.71 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 2-143; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: Y
Molecule details ›
Chain: Y
Length: 133 amino acids
Theoretical weight: 15.46 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TS40 (Residues: 1-133; Coverage: 100%)
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25 Chain: Z
Molecule details ›
Chain: Z
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 1-124; Coverage: 100%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS26 Chain: a
Molecule details ›
Chain: a
Length: 115 amino acids
Theoretical weight: 13.05 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: b
Molecule details ›
Chain: b
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: c
Molecule details ›
Chain: c
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: d
Molecule details ›
Chain: d
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 eS30 Chain: e
Molecule details ›
Chain: e
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Ubiquitin-ribosomal protein eS31 fusion protein Chain: f
Molecule details ›
Chain: f
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 50-188; Coverage: 74%)
Gene name: RPS27A
Sequence domains:
Small ribosomal subunit protein RACK1 Chain: g
Molecule details ›
Chain: g
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 117-424; Coverage: 73%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
18S Ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 1869 nucleotides
Theoretical weight: 602.78 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 9Å
Relevant EMDB volumes: EMD-2810

Quick links

Citations

20 review citations

RAN translation-What makes it run?
Green et al. (2016)
19 more

2 mentions without citation

Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES.
Muhs et al. (2015)
1 more