› 5edn

X-ray diffraction
3.2Å resolution

Structure of HOXB13-DNA(TCG) complex

Released:
DOI: 10.2210/pdb5edn/pdb
PDB entry 5edn coloured by chain, front view.
PDB entry 5edn coloured by chain, side view.
PDB entry 5edn coloured by chain, top view.
Source organisms:
Primary publication:
Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J
Elife 7 (2018)
PMID: 29638214

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118625 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homeobox protein Hox-B13 Chains: A, B, G, J
Molecule details ›
Chains: A, B, G, J
Length: 76 amino acids
Theoretical weight: 8.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92826 (Residues: 209-284; Coverage: 27%)
Gene name: HOXB13
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3') Chains: C, D, H, K
Molecule details ›
Chains: C, D, H, K
Length: 19 nucleotides
Theoretical weight: 5.86 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3') Chains: E, F, I, L
Molecule details ›
Chains: E, F, I, L
Length: 19 nucleotides
Theoretical weight: 5.79 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P2221
Unit cell:
a: 52.618Å b: 52.522Å c: 389.331Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.216 0.281
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Effects of External Perturbations on Protein Systems: A Microscopic View.
Dutta et al. (2022)
1 more

1 mention without citation

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Morgunova et al. (2018)