› 5guh

X-ray diffraction
2.4Å resolution

Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA

Released:
DOI: 10.2210/pdb5guh/pdb
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PDB entry 5guh coloured by chain, front view.
PDB entry 5guh coloured by chain, side view.
PDB entry 5guh coloured by chain, top view.
Source organism: Bombyx mori
Primary publication:
Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA.
Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O
Cell 167 484-497.e9 (2016)
PMID: 27693359

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108605 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Piwi-like protein Siwi Chain: A
Molecule details ›
Chain: A
Length: 899 amino acids
Theoretical weight: 101.48 KDa
Source organism: Bombyx mori
UniProt:
  • Canonical: A8D8P8 (Residues: 1-899; Coverage: 100%)
Gene name: Siwi
Sequence domains:
RNA (28-MER) Chain: B
Molecule details ›
Chain: B
Length: 28 nucleotides
Theoretical weight: 9.03 KDa
Source organism: Bombyx mori

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand OMU 1 x OMU

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 61.899Å b: 114.619Å c: 136.718Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.236

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Citations

13 review citations

PIWI-interacting RNAs: small RNAs with big functions.
Ozata et al. (2019)
12 more

8 mentions without citation

Structural Foundations of RNA Silencing by Argonaute.
Sheu-Gruttadauria et al. (2017)
7 more

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