› 5mey

X-ray diffraction
2.05Å resolution

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

Released:
DOI: 10.2210/pdb5mey/pdb
PDB entry 5mey coloured by chain, front view.
PDB entry 5mey coloured by chain, side view.
PDB entry 5mey 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-119019 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Mothers against decapentaplegic homolog 4 Chain: A
Molecule details ›
Chain: A
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*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.52 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand CL 4 x CL
Ligand PEG 2 x PEG
Ligand EDO 1 x EDO
Ligand CA 5 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2221
Unit cell:
a: 64.17Å b: 79Å c: 90.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.238
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

3 mentions without citation

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