› 7c6b

X-ray diffraction
1.7Å resolution

Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate

Released:
DOI: 10.2210/pdb7c6b/pdb
Model geometry
Fit model/data
PDB entry 7c6b coloured by chain, front view.
PDB entry 7c6b coloured by chain, side view.
PDB entry 7c6b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima T, Sawada T, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, Saito JI
OpenAccess logo RNA 27 163-173 (2021)
PMID: 33177188

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193864 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein argonaute-2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 139 amino acids
Theoretical weight: 15.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKV8 (Residues: 440-578; Coverage: 16%)
Gene names: AGO2, EIF2C2
Sequence domains: Mid domain of argonaute

Ligands and Environments

2 bound ligands:
Ligand K2R 3 x K2R
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P1
Unit cell:
a: 47.28Å b: 66.46Å c: 40.42Å
α: 107.06° β: 95.63° γ: 86.4°
R-values:
R R work R free
0.196 0.194 0.229
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Pre-Clinical and Clinical Applications of Small Interfering RNAs (siRNA) and Co-Delivery Systems for Pancreatic Cancer Therapy.
Mirzaei et al. (2021)
1 other article

1 mention without citation

siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
Shinohara et al. (2021)