› 4z4d

X-ray diffraction
1.6Å resolution

Human Argonaute2 Bound to t1-G Target RNA

Released:
DOI: 10.2210/pdb4z4d/pdb
PDB entry 4z4d coloured by chain, front view.
PDB entry 4z4d coloured by chain, side view.
PDB entry 4z4d coloured by chain, top view.
Source organisms:
Primary publication:
Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ
Elife 4 (2015)
PMID: 26359634

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193874 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Protein argonaute-2 Chain: A
Molecule details ›
Chain: A
Length: 859 amino acids
Theoretical weight: 97.38 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UKV8 (Residues: 1-859; Coverage: 100%)
Gene names: AGO2, EIF2C2
Sequence domains:
Structure domains:
RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.55 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.55 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand IPH 4 x IPH
Ligand IPA 5 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P21
Unit cell:
a: 55.738Å b: 117.016Å c: 69.874Å
α: 90° β: 92.43° γ: 90°
R-values:
R R work R free
0.164 0.163 0.189
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

15 review citations

Metazoan MicroRNAs.
Bartel DP. (2018)
14 more

14 mentions without citation

A Structural View of miRNA Biogenesis and Function.
Leitão et al. (2022)
13 more