› 4hje

X-ray diffraction
1.91Å resolution

Crystal structure of p53 core domain in complex with DNA

Released:
DOI: 10.2210/pdb4hje/pdb
PDB entry 4hje coloured by chain, front view.
PDB entry 4hje coloured by chain, side view.
PDB entry 4hje coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion.
Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L
Nucleic Acids Res 41 8368-76 (2013)
PMID: 23836939

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117599 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Cellular tumor antigen p53 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 200 amino acids
Theoretical weight: 22.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04637 (Residues: 92-291; Coverage: 51%)
Gene names: P53, TP53
Sequence domains: P53 DNA-binding domain
Structure domains: Immunoglobulin-like
DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 65.42Å b: 93.88Å c: 145.634Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Absence of a simple code: how transcription factors read the genome.
Slattery et al. (2014)
6 more

28 mentions without citation

Intracellular pH Regulates Cancer and Stem Cell Behaviors: A Protein Dynamics Perspective.
Liu et al. (2020)
27 more