› 2vrt

X-ray diffraction
3.5Å resolution

Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain

Released:
DOI: 10.2210/pdb2vrt/pdb
PDB entry 2vrt coloured by chain, front view.
PDB entry 2vrt coloured by chain, side view.
PDB entry 2vrt coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation.
Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF
Structure 16 1238-44 (2008)
PMID: 18682225

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149270 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Ribonuclease E Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 509 amino acids
Theoretical weight: 57.28 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21513 (Residues: 1-509; Coverage: 48%)
Gene names: JW1071, ams, b1084, hmp1, rne
Sequence domains:
Structure domains: Ribonuclease E, catalytic domain
5'-R(*UP*UP)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 2 nucleotides
Theoretical weight: 567 Da
Source organism: Escherichia coli
Expression system: Not provided
5'-R(*UP*UP*GP)-3' Chains: G, H
Molecule details ›
Chains: G, H
Length: 3 nucleotides
Theoretical weight: 913 Da
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 93.894Å b: 121.252Å c: 242.228Å
α: 90° β: 99.47° γ: 90°
R-values:
R R work R free
0.321 0.317 0.351
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

18 review citations

The critical role of RNA processing and degradation in the control of gene expression.
Arraiano et al. (2010)
17 more

1 mention without citation

Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity.
Murashko et al. (2012)