› 3hsb

X-ray diffraction
2.2Å resolution

Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer

Released:
DOI: 10.2210/pdb3hsb/pdb
PDB entry 3hsb coloured by chain, front view.
PDB entry 3hsb coloured by chain, side view.
PDB entry 3hsb coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq.
Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K
Nucleic Acids Res 40 1856-67 (2012)
PMID: 22053080

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128372 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
RNA-binding protein Hfq Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 78 amino acids
Theoretical weight: 8.93 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O31796 (Residues: 1-73; Coverage: 100%)
Gene names: BSU17340, hfq, ymaH
Sequence domains: Hfq protein
Structure domains: SH3 type barrels.
RNA (5'-R(*AP*GP*AP*GP*AP*GP*A)-3') Chain: X
Molecule details ›
Chain: X
Length: 7 nucleotides
Theoretical weight: 2.31 KDa
Source organism: Bacillus subtilis
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: I422
Unit cell:
a: 123.7Å b: 123.7Å c: 119.131Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Hfq: the flexible RNA matchmaker.
Updegrove et al. (2016)
12 more

10 mentions without citation

Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches.
Ruigrok et al. (2012)
9 more