› 6p4f

X-ray diffraction
3.55Å resolution

Crystal structure of the XPB-Bax1-forked DNA ternary complex

Released:
DOI: 10.2210/pdb6p4f/pdb
PDB entry 6p4f coloured by chain, front view.
PDB entry 6p4f coloured by chain, side view.
PDB entry 6p4f coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Primary publication:
Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA.
He F, DuPrez K, Hilario E, Chen Z, Fan L
Nucleic Acids Res 48 11695-11705 (2020)
PMID: 32986831

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120435 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA 3'-5' translocase XPB2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 440 amino acids
Theoretical weight: 50.73 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q970I2 (Residues: 1-439; Coverage: 100%)
Gene names: ST1613, STK_16130, xpb2
Sequence domains:
Endonuclease Bax1 Chains: B, D
Molecule details ›
Chains: B, D
Length: 373 amino acids
Theoretical weight: 44.32 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q970I1 (Residues: 2-372; Coverage: 77%)
Gene names: ST1614, STK_16140, bax1
Sequence domains: Protein of unknown function (DUF790)
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*TP*TP*TP*GP*CP*TP*AP*CP*AP*A)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 24 nucleotides
Theoretical weight: 7.26 KDa
DNA (5'-D(P*TP*GP*TP*AP*GP*GP*TP*TP*TP*CP*CP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 23 nucleotides
Theoretical weight: 7.09 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 25 x MG
Ligand CL 11 x CL
Ligand PO4 3 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 214.687Å b: 92.15Å c: 172.128Å
α: 90° β: 132.24° γ: 90°
R-values:
R R work R free
0.251 0.25 0.272
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex.
Marshall et al. (2022)

1 mention without citation

Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA.
He et al. (2020)