› 4prf

X-ray diffraction
2.4Å resolution

A Second Look at the HDV Ribozyme Structure and Dynamics.

Released:
DOI: 10.2210/pdb4prf/pdb
PDB entry 4prf coloured by chain, front view.
PDB entry 4prf coloured by chain, side view.
PDB entry 4prf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS
Nucleic Acids Res 42 12833-46 (2014)
PMID: 25326328

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140501 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chain: A
Molecule details ›
Chain: A
Length: 100 amino acids
Theoretical weight: 11.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 1-100; Coverage: 36%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
Hepatitis Delta virus ribozyme Chain: B
Molecule details ›
Chain: B
Length: 76 nucleotides
Theoretical weight: 24.47 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: R32
Unit cell:
a: 108.944Å b: 108.944Å c: 191.754Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.198 0.252
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.
Zhou et al. (2015)
1 more

3 mentions without citation

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
2 more