5MEY: Smad4-MH1

Name: PDB 5MEY: Crystal structure of Smad4-MH1 bound to the GGCGC site.
Published: 2017-11-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of Smad4-MH1 bound to the GGCGC site. Determined by X-ray diffraction at 2.05 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,468
Mol. weight: 21.44 kDa
Ligands: ZN, CA
Released: 15 Nov 2017

Explore 5MEY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MEY contains 7 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	16-24	9
α-helix	33-47	15
α-helix	51-62	12
β-strand	73-75	3	1
α-helix	76-77	2
β-strand	82-84	3	2
β-strand	87-89	3	2
α-helix	91-99	9
β-strand	109-111	3	3
α-helix	119-121	3
β-strand	125-127	3	1
α-helix	130-132	3
β-strand	133-135	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MH1 domain of human Smad4	A	protein	135	Homo sapiens	Q13485 (AlphaFold model)
DNA (5'-d(paptpgpcpgpgpgpcpgpcpgpcpcpcpgpcpapt)-3')	D	DNA	18	Homo sapiens

Sequence of entity 1 (A), FASTA

>5MEY_1 MH1 domain of human Smad4 (chains A)
GAMGPTSNDACLSIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNG
AHPSKCVTIQRTLDGRLQVAGRKGFPHVIYARLWRWPDLHKNELKHVKYCQYAFDLKCDS
VCVNPYHYERVVSPG

Sequence of entity 2 (D), FASTA

>5MEY_2 DNA (5'-D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3') (chains D)
ATGCGGGCGCGCCCGCAT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	5

Water and common crystallization additives (CL, PEG, EDO) are not listed.

Primary citation

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. Martin-Malpartida, P., Batet, M., Kaczmarska, Z. et al. Nat Commun (2017) 8:2070-2070. DOI 10.1038/s41467-017-02054-6 · PubMed

Other PDB entries of the same protein (UniProt Q13485 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YIC 1.6 Å, 14-3-3 sigma in complex with SMAD4 pS403 peptide
9HWE 1.7 Å, SMAD4 MH2, residues 314-552
9HZA 2.03 Å, SMAD4 MH2, residues 272-552
1YGS 2.1 Å, Crystal structure of the SMAD4 tumor suppressor C-terminal domain
9QE6 2.1 Å, SMAD4 MH2 domain (residues 314-552) bound by Nanobody A1 (NbA1)
5UWU 2.24 Å, Crystal Structure of SMAD4 NES Peptide in complex with CRM1-Ran-RanBP1
1U7F 2.6 Å, Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
5C4V 2.6 Å, Ski-like protein
1DD1 2.62 Å, Crystal structure analysis of the SMAD4 active fragment
1U7V 2.7 Å, Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex
1MR1 2.85 Å, Crystal Structure of a Smad4-Ski Complex
5MEZ 2.98 Å, Crystal structure of Smad4-MH1 bound to the GGCT site.

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