5ODG: Smad3-MH1

Name: PDB 5ODG: Crystal structure of Smad3-MH1 bound to the GGCT site.
Published: 2017-11-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of Smad3-MH1 bound to the GGCT site. Determined by X-ray diffraction at 2.12 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,643
Mol. weight: 40.04 kDa
Ligands: ZN
Released: 15 Nov 2017

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

Secondary structure: helices and β-sheets

5ODG contains 17 α-helices and 12 β-strands across 2 chains. 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
α-helix	25-45	21
α-helix	48-57	10
β-strand	66-68	3	1
α-helix	69-70	2
β-strand	75-77	3	2
β-strand	80-82	3	2
α-helix	84-92	9
α-helix	100-102	3
β-strand	103-105	3	3
α-helix	113-115	3
β-strand	119-121	3	1
α-helix	124-126	3
β-strand	127-129	3	3
α-helix	131-133	3

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
α-helix	25-45	21
α-helix	48-57	10
β-strand	66-68	3	4
α-helix	69-70	2
β-strand	75-77	3	5
β-strand	80-82	3	5
α-helix	84-92	9
α-helix	100-102	3
β-strand	103-105	3	6
α-helix	113-115	3
β-strand	119-121	3	4
α-helix	124-126	3
β-strand	127-129	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mothers against decapentaplegic homolog 3	A, B	protein	128	Homo sapiens	P84022 (AlphaFold model)
DNA (5'-d(pcpapgpgpcptpapgpcpcptpgpcpa)-3')	D, E	DNA	16	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5ODG_1 Mothers against decapentaplegic homolog 3 (chains A, B)
GAMIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITI
PRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHY
QRVETPVL

Sequence of entity 2 (D, E), FASTA

>5ODG_2 DNA (5'-D(P*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3') (chains D, E)
TGCAGGCTAGCCTGCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (CL) 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 P84022 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YIB 1.7 Å, 14-3-3 sigma in complex with SMAD3 pS423 peptide
1MJS 1.91 Å, MH2 domain of transcriptional factor SMAD3
5OD6 2.0 Å, Crystal structure of Smad3-MH1 bound to the GGCGC site.
6ZMN 2.33 Å, Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site
1OZJ 2.4 Å, Crystal structure of Smad3-MH1 bound to DNA at 2.4 A resolution
5XOC 2.4 Å, Crystal structure of human Smad3-FoxH1 complex
1U7F 2.6 Å, Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
1MK2 2.74 Å, SMAD3 SBD complex
1MHD 2.8 Å, Crystal structure of a smad MH1 domain bound to DNA
2LAJ Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3…
2LB2 Structure of the second domain of human Nedd4L in complex with a phosphorylated pTPY…

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