› 3nm9

X-ray diffraction
2.85Å resolution

HMGD(M13A)-DNA complex

Released:
DOI: 10.2210/pdb3nm9/pdb
PDB entry 3nm9 coloured by chain, front view.
PDB entry 3nm9 coloured by chain, side view.
PDB entry 3nm9 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending.
Churchill MEA, Klass J, Zoetewey DL
J Mol Biol 403 88-102 (2010)
PMID: 20800069

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116625 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
High mobility group protein D Chains: A, D, G, J, M, P
Molecule details ›
Chains: A, D, G, J, M, P
Length: 73 amino acids
Theoretical weight: 8.31 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05783 (Residues: 2-74; Coverage: 65%)
Gene names: CG17950, HmgD
Sequence domains: HMG (high mobility group) box
Structure domains: High mobility group box domain
DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' Chains: B, C, E, F, H, I, K, L, N, O
Molecule details ›
Chains: B, C, E, F, H, I, K, L, N, O
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P1
Unit cell:
a: 44.75Å b: 71.7Å c: 89.02Å
α: 92.49° β: 91.12° γ: 107.1°
R-values:
R R work R free
0.248 0.245 0.296
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

The high mobility group box: the ultimate utility player of a cell.
Malarkey et al. (2012)
3 more

3 mentions without citation

The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose).
Silva et al. (2016)
2 more