› 4qr9

X-ray diffraction
2Å resolution

Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA

Released:
DOI: 10.2210/pdb4qr9/pdb
PDB entry 4qr9 coloured by chain, front view.
PDB entry 4qr9 coloured by chain, side view.
PDB entry 4qr9 coloured by chain, top view.
Source organisms:
Primary publication:
Two high-mobility group box domains act together to underwind and kink DNA.
Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL
Acta Crystallogr D Biol Crystallogr 71 1423-32 (2015)
PMID: 26143914

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118030 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
High mobility group protein B1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 76 amino acids
Theoretical weight: 8.95 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P63159 (Residues: 8-81; Coverage: 34%)
Gene names: Hmg-1, Hmg1, Hmgb1
Sequence domains: HMG-box domain
Structure domains: High mobility group box domain
DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') Chains: C, D, E, F
Molecule details ›
Chains: C, D, E, F
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P212121
Unit cell:
a: 42.751Å b: 84.17Å c: 94.227Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Immunological Significance of HMGB1 Post-Translational Modification and Redox Biology.
Kwak et al. (2020)
6 more

6 mentions without citation

Studying protein-DNA interactions using atomic force microscopy.
Beckwitt et al. (2018)
5 more