› 1jbr

X-ray diffraction
2.15Å resolution

Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor

Released:
DOI: 10.2210/pdb1jbr/pdb
PDB entry 1jbr coloured by chain, front view.
PDB entry 1jbr coloured by chain, side view.
PDB entry 1jbr coloured by chain, top view.
Source organism: Aspergillus restrictus
Primary publication:
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
Yang X, Gérczei T, Glover LT, Correll CC
Nat Struct Biol 8 968-73 (2001)
PMID: 11685244

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-219412 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct RNA molecules
Macromolecules (4 distinct):
Ribonuclease mitogillin Chains: A, B
Molecule details ›
Chains: A, B
Length: 149 amino acids
Theoretical weight: 16.89 KDa
Source organism: Aspergillus restrictus
UniProt:
  • Canonical: P67876 (Residues: 28-176; Coverage: 100%)
Gene name: ret
Structure domains: Microbial ribonucleases
5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3' Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.81 KDa
Source organism: Aspergillus restrictus
Expression system: Not provided
5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3' Chain: F
Molecule details ›
Chain: F
Length: 13 nucleotides
Theoretical weight: 4.23 KDa
Source organism: Aspergillus restrictus
Expression system: Not provided
31-mer SRD RNA analog Chain: D
Molecule details ›
Chain: D
Length: 31 nucleotides
Theoretical weight: 10.03 KDa
Source organism: Aspergillus restrictus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand K 5 x K
1 modified residue:
Ligand A23 1 x A23

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P21
Unit cell:
a: 60.4Å b: 109.7Å c: 40Å
α: 90° β: 97.8° γ: 90°
R-values:
R R work R free
0.238 0.232 0.29
Expression system: Not provided

Quick links

Citations

10 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
9 more

12 mentions without citation

Recognition modes of RNA tetraloops and tetraloop-like motifs by RNA-binding proteins.
Thapar et al. (2014)
11 more