› 7a01

Electron Microscopy
3.6Å resolution

The Halastavi arva virus intergenic region IRES promotes translation by the simplest possible initiation mechanism

Released:
DOI: 10.2210/pdb7a01/pdb
PDB entry 7a01 coloured by chain, front view.
PDB entry 7a01 coloured by chain, side view.
PDB entry 7a01 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.
Abaeva IS, Vicens Q, Bochler A, Soufari H, Simonetti A, Pestova TV, Hashem Y, Hellen CUT
Cell Rep 33 108476 (2020)
PMID: 33296660
Related structures: EMD-11590

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 85-mer (preferred)
PDBe Complex ID:
PDB-CPX-243856 (preferred)
Entry contents:
80 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (85 distinct):
Large ribosomal subunit protein eL38 Chain: p2
Molecule details ›
Chain: p2
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U001 (Residues: 2-70; Coverage: 99%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein uL14 Chain: k2
Molecule details ›
Chain: k2
Length: 131 amino acids
Theoretical weight: 13.97 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T6D1 (Residues: 10-140; Coverage: 94%)
Gene name: RPL23
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24 Chain: l2
Large ribosomal subunit protein uL23 Chain: m2
Large ribosomal subunit protein uL24 Chain: o2
Large ribosomal subunit protein uL15 Chain: q2
Large ribosomal subunit protein eL29 Chain: r2
Large ribosomal subunit protein uL4 Chain: t2
Large ribosomal subunit protein eL31 Chain: u2
Large ribosomal subunit protein eL32 Chain: v2
Large ribosomal subunit protein uL13 Chain: w2
Large ribosomal subunit protein eL33 Chain: x2
Large ribosomal subunit protein eL34 Chain: y2
Large ribosomal subunit protein uL2 Chain: 92
Large ribosomal subunit protein uL29 Chain: A2
Large ribosomal subunit protein eL36 Chain: B2
Large ribosomal subunit protein eL37 Chain: C2
Large ribosomal subunit protein eL39 Chain: D2
Large ribosomal subunit protein eL40 Chain: E2
Large ribosomal subunit protein eL42 Chain: F2
Large ribosomal subunit protein uL18 Chain: G2
Large ribosomal subunit protein uL22 Chain: H2
Large ribosomal subunit protein eL43 Chain: I2
Large ribosomal subunit protein eL28 Chain: J2
Large ribosomal subunit protein uL10 Chain: K2
Large ribosomal subunit protein uL16 Chain: L2
Large ribosomal subunit protein uL11 Chain: M2
Large ribosomal subunit protein eL6 Chain: R2
Large ribosomal subunit protein eL18 Chain: S2
Large ribosomal subunit protein eL6 Chain: T2
Large ribosomal subunit protein uL30 Chain: U2
Large ribosomal subunit protein eL8 Chain: V2
Large ribosomal subunit protein uL6 Chain: W2
Large ribosomal subunit protein uL16 Chain: X2
Large ribosomal subunit protein uL5 Chain: Y2
Large ribosomal subunit protein eL14 Chain: 02
Large ribosomal subunit protein eL15 Chain: 12
Large ribosomal subunit protein eL27 Chain: 22
Large ribosomal subunit protein eL19 Chain: 32
Large ribosomal subunit protein uL1 Chain: 42
Large ribosomal subunit protein uL3 Chain: 52
Large ribosomal subunit protein eL20 Chain: 62
Large ribosomal subunit protein eL21 Chain: 72
Large ribosomal subunit protein eL22 Chain: 82
Small ribosomal subunit protein eS30 Chain: s3
Large ribosomal subunit protein eL30 Chain: 13
Ubiquitin-ribosomal protein eS31 fusion protein Chain: Q3
Small ribosomal subunit protein uS17 Chain: G3
Small ribosomal subunit protein uS13 Chain: G5
Small ribosomal subunit protein RACK1 Chain: a3
Small ribosomal subunit protein uS11 Chain: a5
Small ribosomal subunit protein uS19 Chain: A3
Small ribosomal subunit protein uS12 Chain: T3
40S ribosomal protein SA Chain: U3
Small ribosomal subunit protein eS1 Chain: V3
S5 DRBM domain-containing protein Chain: W3
Small ribosomal subunit protein eS32 Chain: X3
Small ribosomal subunit protein uS3 Chain: Y3
Small ribosomal subunit protein eS4 Chain: j3
Small ribosomal subunit protein uS8 Chain: J5
Small ribosomal subunit protein uS7 Chain: N3
Small ribosomal subunit protein eS6 Chain: b3
Small ribosomal subunit protein uS9 Chain: B3
Small ribosomal subunit protein eS28 Chain: f3
Small ribosomal subunit protein uS15 Chain: F3
Small ribosomal subunit protein eS8 Chain: c3
Small ribosomal subunit protein eS17 Chain: C3
Small ribosomal subunit protein uS4 Chain: d3
Small ribosomal subunit protein eS21 Chain: D3
Small ribosomal subunit protein eS12 Chain: e3
Small ribosomal subunit protein eS10 Chain: E3
Small ribosomal subunit protein uS14 Chain: H3
Small ribosomal subunit protein eS19 Chain: H5
Small ribosomal subunit protein eS7 Chain: P3
Small ribosomal subunit protein uS10 Chain: I3
40S ribosomal protein S24 Chain: I5
Small ribosomal subunit protein eS27 Chain: L3
Small ribosomal subunit protein eS25 Chain: M3
Small ribosomal subunit protein eS26 Chain: O3
60S ribosomal protein L13 Chain: a7
INTERNAL RIBOSOME ENTRY SITE Chain: E1
28S ribosomal RNA Chain: e2
5.8S ribosomal RNA Chain: h2
5S ribosomal RNA Chain: d2
18S Ribosomal RNA Chain: K3

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.6Å
Relevant EMDB volumes: EMD-11590

Quick links

Citations

3 review citations

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

2 mentions without citation

The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.
Abaeva et al. (2020)
1 more