› 6w2s

Electron Microscopy
3.47Å resolution

Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)

Released:
DOI: 10.2210/pdb6w2s/pdb
PDB entry 6w2s coloured by chain, front view.
PDB entry 6w2s coloured by chain, side view.
PDB entry 6w2s coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.
Neupane R, Pisareva VP, Rodriguez CF, Pisarev AV, Fernández IS
Elife 9 (2020)
PMID: 32286223
Related structures: EMD-21529

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 43-mer (preferred)
PDBe Complex ID:
PDB-CPX-242525 (preferred)
Entry contents:
41 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (43 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 295 amino acids
Theoretical weight: 33.02 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 1-295; Coverage: 100%)
Gene name: RPSA
Sequence domains:
Small ribosomal subunit protein eS1 Chain: C
Molecule details ›
Chain: C
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
Small ribosomal subunit protein uS5 Chain: D
Molecule details ›
Chain: D
Length: 255 amino acids
Theoretical weight: 27.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SWM1 (Residues: 1-190, 192-292; Coverage: 87%)
Gene name: RPS2
Sequence domains:
Small ribosomal subunit protein eS4 Chain: F
Molecule details ›
Chain: F
Length: 263 amino acids
Theoretical weight: 29.6 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TK17 (Residues: 1-263; Coverage: 100%)
Gene name: RPS4X
Sequence domains:
Small ribosomal subunit protein eS6 Chain: H
Molecule details ›
Chain: H
Length: 249 amino acids
Theoretical weight: 28.75 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM55 (Residues: 1-249; Coverage: 100%)
Gene name: RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: I
Molecule details ›
Chain: I
Length: 194 amino acids
Theoretical weight: 22.17 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 1-194; Coverage: 100%)
Gene name: RPS7
Small ribosomal subunit protein eS8 Chain: J
Molecule details ›
Chain: J
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: K
Molecule details ›
Chain: K
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 uS17 Chain: M
Molecule details ›
Chain: M
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 uS15 Chain: O
Molecule details ›
Chain: O
Length: 151 amino acids
Theoretical weight: 17.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 1-151; Coverage: 100%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chain: P
Molecule details ›
Chain: P
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
eS21 Chain: W
Molecule details ›
Chain: W
Length: 83 amino acids
Theoretical weight: 9.1 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS8 Chain: X
Molecule details ›
Chain: X
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: Y
Molecule details ›
Chain: Y
Length: 143 amino acids
Theoretical weight: 15.78 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: Z
Molecule details ›
Chain: Z
Length: 134 amino acids
Theoretical weight: 15.55 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T3D8 (Residues: 1-131; Coverage: 100%)
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS26 Chain: b
Molecule details ›
Chain: b
Length: 115 amino acids
Theoretical weight: 13.02 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
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein Chain: f
Molecule details ›
Chain: f
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:
Small ribosomal subunit protein uS3 Chain: E
Molecule details ›
Chain: E
Length: 281 amino acids
Theoretical weight: 31.15 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 1-243; Coverage: 100%)
Gene name: RPS3
Sequence domains:
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
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 eS10 Chain: L
Molecule details ›
Chain: L
Length: 149 amino acids
Theoretical weight: 17.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPV3 (Residues: 1-149; Coverage: 90%)
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein eS12 Chain: N
Molecule details ›
Chain: N
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 uS19 Chain: Q
Molecule details ›
Chain: Q
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: R
Molecule details ›
Chain: R
Length: 172 amino acids
Theoretical weight: 19.21 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 1-146; Coverage: 100%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
Length: 145 amino acids
Theoretical weight: 16.24 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: V
Molecule details ›
Chain: V
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 eS25 Chain: a
Molecule details ›
Chain: a
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 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
Ubiquitin-ribosomal protein eS31 fusion protein Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 18 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 1-156; Coverage: 100%)
Gene name: RPS27A
Sequence domains:
Small ribosomal subunit protein RACK1 Chain: h
Molecule details ›
Chain: h
Length: 317 amino acids
Theoretical weight: 35.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 1-317; Coverage: 100%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
Eukaryotic translation initiation factor 3 subunit A Chain: 1
Molecule details ›
Chain: 1
Length: 1362 amino acids
Theoretical weight: 164.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SMZ5 (Residues: 1-1362; Coverage: 100%)
Gene names: EIF3A, EIF3S10
Sequence domains: PCI domain
Eukaryotic translation initiation factor 3 subunit C Chain: 2
Molecule details ›
Chain: 2
Length: 913 amino acids
Theoretical weight: 105.71 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U971 (Residues: 1-913; Coverage: 100%)
Gene names: EIF3C, EIF3S8
Sequence domains:
Eukaryotic translation initiation factor 3 subunit E Chain: 3
Molecule details ›
Chain: 3
Length: 462 amino acids
Theoretical weight: 54.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SUC8 (Residues: 1-462; Coverage: 100%)
Gene names: EIF3E, EIF3S6, INT6
Sequence domains:
Eukaryotic translation initiation factor 3 subunit F Chain: 4
Molecule details ›
Chain: 4
Length: 364 amino acids
Theoretical weight: 37.85 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SLC2 (Residues: 1-364; Coverage: 100%)
Gene names: EIF3F, EIF3S5
Sequence domains:
Eukaryotic translation initiation factor 3 subunit H Chain: 5
Molecule details ›
Chain: 5
Length: 363 amino acids
Theoretical weight: 41.08 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1ST95 (Residues: 1-363; Coverage: 100%)
Gene names: EIF3H, EIF3S3
Sequence domains:
Eukaryotic translation initiation factor 3 subunit K Chain: 6
Molecule details ›
Chain: 6
Length: 218 amino acids
Theoretical weight: 25.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T3L2 (Residues: 1-218; Coverage: 100%)
Gene names: EIF3K, EIF3S12
Sequence domains: CSN8/PSMD8/EIF3K family
Eukaryotic translation initiation factor 3 subunit L Chain: 7
Molecule details ›
Chain: 7
Length: 607 amino acids
Theoretical weight: 71 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SED9 (Residues: 1-607; Coverage: 100%)
Gene names: EIF3EIP, EIF3L, EIF3S6IP
Sequence domains: RNA polymerase I-associated factor PAF67
Eukaryotic translation initiation factor 3 subunit M Chain: 8
Molecule details ›
Chain: 8
Length: 374 amino acids
Theoretical weight: 42.56 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SLW8 (Residues: 1-374; Coverage: 100%)
Gene name: EIF3M
Sequence domains:
18S Ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1697 nucleotides
Theoretical weight: 547.73 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
CrPV 5'-UTR IRES Chain: 0
Molecule details ›
Chain: 0
Length: 377 nucleotides
Theoretical weight: 121.09 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.47Å
Relevant EMDB volumes: EMD-21529

Quick links

Citations

5 review citations

Non-Canonical Translation Initiation Mechanisms Employed by Eukaryotic Viral mRNAs.
Sorokin et al. (2021)
4 more

2 mentions without citation

A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.
Neupane et al. (2020)
1 more