› 5x6m

X-ray diffraction
3.2Å resolution

Crystal Structure of SMAD5-MH1 in complex with a composite DNA sequence

Released:
DOI: 10.2210/pdb5x6m/pdb
PDB entry 5x6m coloured by chain, front view.
PDB entry 5x6m coloured by chain, side view.
PDB entry 5x6m coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.
Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW
Nucleic Acids Res 43 9051-64 (2015)
PMID: 26304548

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119381 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Mothers against decapentaplegic homolog 5 Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 150 amino acids
Theoretical weight: 17.32 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P97454 (Residues: 1-143; Coverage: 31%)
Gene names: Madh5, Msmad5, Smad5
Sequence domains: MH1 domain
Structure domains: SMAD MH1 domain
DNA (5'-D(P*AP*TP*CP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*AP*TP*A)-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 22 nucleotides
Theoretical weight: 6.74 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*TP*AP*TP*AP*GP*AP*CP*TP*GP*CP*CP*GP*GP*CP*AP*GP*TP*CP*TP*GP*A)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 22 nucleotides
Theoretical weight: 6.77 KDa
Source organism: synthetic construct
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: SSRF BEAMLINE BL17U
Spacegroup: P31
Unit cell:
a: 119.464Å b: 119.464Å c: 93.067Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.21 0.253
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Specification of BMP Signaling.
Nickel et al. (2019)
5 more