› 5d9i

X-ray diffraction
1.7Å resolution

SV40 Large T antigen origin binding domain bound to artificial DNA fork

Released:
DOI: 10.2210/pdb5d9i/pdb
PDB entry 5d9i coloured by chain, front view.
PDB entry 5d9i coloured by chain, side view.
PDB entry 5d9i coloured by chain, top view.
Source organisms:
Primary publication:
Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA.
Meinke G, Phelan PJ, Fradet-Turcotte A, Bohm A, Archambault J, Bullock PA
J Virol 85 818-27 (2011)
PMID: 20980496

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118547 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Large T antigen Chains: A, B
Molecule details ›
Chains: A, B
Length: 134 amino acids
Theoretical weight: 15.49 KDa
Source organism: Macaca mulatta polyomavirus 1
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P03070 (Residues: 131-260; Coverage: 18%)
Sequence domains: Origin of replication binding protein
Structure domains: Replication Protein E1; Chain: A,
DNA (5'-D(*GP*AP*GP*GP*AP*GP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*AP*GP*GP*CP*C)-3') Chain: X
Molecule details ›
Chain: X
Length: 21 nucleotides
Theoretical weight: 6.55 KDa
Source organism: synthetic construct
Expression system: synthetic construct
DNA (5'-D(*AP*CP*TP*CP*CP*TP*CP*CP*GP*AP*AP*AP*AP*AP*AP*CP*CP*TP*CP*CP*GP*GP*A)-3') Chain: Y
Molecule details ›
Chain: Y
Length: 23 nucleotides
Theoretical weight: 6.96 KDa
Source organism: synthetic construct
Expression system: synthetic construct

Ligands and Environments

3 bound ligands:
Ligand EDO 2 x EDO
Ligand CA 2 x CA
Ligand ACT 1 x ACT
1 modified residue:
Ligand CME 2 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2
Unit cell:
a: 94.192Å b: 63.393Å c: 64.891Å
α: 90° β: 92.42° γ: 90°
R-values:
R R work R free
0.182 0.18 0.223
Expression systems:
  • Escherichia coli BL21
  • synthetic construct

Quick links

Citations

2 review citations

Genome analysis of the new human polyomaviruses.
Van Ghelue et al. (2012)
1 more

1 mention without citation

Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains.
Meinke et al. (2016)