› 5mez

X-ray diffraction
2.98Å resolution

Crystal structure of Smad4-MH1 bound to the GGCT site.

Released:
DOI: 10.2210/pdb5mez/pdb
PDB entry 5mez coloured by chain, front view.
PDB entry 5mez coloured by chain, side view.
PDB entry 5mez coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragón E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Márquez JA, Massagué J, Macias MJ
Nat Commun 8 2070 (2017)
PMID: 29234012

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119020 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Mothers against decapentaplegic homolog 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 135 amino acids
Theoretical weight: 15.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13485 (Residues: 10-140; Coverage: 24%)
Gene names: DPC4, MADH4, SMAD4
Sequence domains: MH1 domain
Structure domains: SMAD MH1 domain
DNA (5'-D(P*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P212121
Unit cell:
a: 64.79Å b: 79.06Å c: 114.16Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.217 0.252
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

Contextual determinants of TGFβ action in development, immunity and cancer.
David et al. (2018)
15 more

2 mentions without citation

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.
Martin-Malpartida et al. (2017)
1 more