› 1rb8

X-ray diffraction
3.5Å resolution

The phiX174 DNA binding protein J in two different capsid environments.

Released:
DOI: 10.2210/pdb1rb8/pdb
PDB entry 1rb8 coloured by chain, front view.
PDB entry 1rb8 coloured by chain, side view.
PDB entry 1rb8 coloured by chain, top view.
Source organisms:
Primary publication:
The phiX174 protein J mediates DNA packaging and viral attachment to host cells.
Bernal RA, Hafenstein S, Esmeralda R, Fane BA, Rossmann MG
J Mol Biol 337 1109-22 (2004)
PMID: 15046981

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 240-mer (preferred)
PDBe Complex ID:
PDB-CPX-114508 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 distinct):
Capsid protein F Chain: F
Molecule details ›
Chain: F
Length: 431 amino acids
Theoretical weight: 49.29 KDa
Source organism: Escherichia phage alpha3
UniProt:
  • Canonical: P08767 (Residues: 1-431; Coverage: 100%)
Gene name: F
Sequence domains: Capsid protein (F protein)
Structure domains: Microviridae F protein
Major spike protein G Chain: G
Molecule details ›
Chain: G
Length: 187 amino acids
Theoretical weight: 19.6 KDa
Source organism: Escherichia phage alpha3
UniProt:
  • Canonical: P31281 (Residues: 1-187; Coverage: 100%)
Gene name: G
Sequence domains: Major spike protein (G protein)
Structure domains: Jelly Rolls
DNA-binding protein J Chain: J
Molecule details ›
Chain: J
Length: 37 amino acids
Theoretical weight: 4.11 KDa
Source organism: Sinsheimervirus phiX174
Expression system: Escherichia coli
UniProt:
  • Canonical: P69592 (Residues: 2-38; Coverage: 97%)
Gene name: J
Sequence domains: Microvirus J protein
DNA (5'-D(P*CP*AP*AP*A)-3') Chain: X
Molecule details ›
Chain: X
Length: 4 nucleotides
Theoretical weight: 1.18 KDa

Ligands and Environments

1 bound ligand:
Ligand DC 6 x DC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: R3
Unit cell:
a: 295.143Å b: 295.143Å c: 678.235Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.234 0.236
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The microviridae: Diversity, assembly, and experimental evolution.
Doore et al. (2016)
14 other articles

5 mentions without citation

A Concise Review of Biomolecule Visualization.
Li et al. (2024)
4 more