› 1ytu

X-ray diffraction
2.5Å resolution

Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein

Released:
DOI: 10.2210/pdb1ytu/pdb
PDB entry 1ytu coloured by chain, front view.
PDB entry 1ytu coloured by chain, side view.
PDB entry 1ytu coloured by chain, top view.
Source organism: Archaeoglobus fulgidus DSM 4304
Primary publication:
Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein.
Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T, Patel DJ
Nature 434 666-70 (2005)
PMID: 15800629

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128085 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Piwi protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 427 amino acids
Theoretical weight: 49.82 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O28951 (Residues: 1-427; Coverage: 100%)
Gene name: AF_1318
Sequence domains: Piwi domain
Structure domains:
5'-R(P*AP*GP*AP*CP*AP*G)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 6 nucleotides
Theoretical weight: 1.94 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Not provided
5'-R(P*UP*GP*UP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
Source organism: Archaeoglobus fulgidus DSM 4304
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: R3
Unit cell:
a: 238.747Å b: 238.747Å c: 52.042Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.204 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

122 review citations

MicroRNAs: target recognition and regulatory functions.
Bartel DP. (2009)
121 more

10 mentions without citation

RNA-binding proteins: modular design for efficient function.
Lunde et al. (2007)
9 more