6ZMN: Smad3-Smad5 MH1 domain chimera

Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site. Determined by X-ray diffraction at 2.33 Å resolution. Released 26 Aug 2020.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,670
Mol. weight: 39.55 kDa
Ligands: ZN
Released: 26 Aug 2020

Explore 6ZMN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZMN contains 19 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
α-helix	19-22	4
α-helix	23-41	19
α-helix	45-54	10
α-helix	60-61	2
β-strand	63-65	3	1
α-helix	66-67	2
β-strand	72-74	3	2
β-strand	77-79	3	2
α-helix	81-89	9
α-helix	97-99	3
β-strand	100-102	3	3
α-helix	110-112	3
β-strand	116-118	3	1
α-helix	121-123	3
β-strand	124-126	3	3

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
α-helix	23-41	19
α-helix	45-54	10
α-helix	60-61	2
β-strand	63-65	3	4
α-helix	66-67	2
β-strand	72-74	3	5
β-strand	77-79	3	5
α-helix	81-89	9
α-helix	97-99	3
β-strand	100-102	3	6
α-helix	110-112	3
β-strand	116-118	3	4
α-helix	121-123	3
β-strand	124-126	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mothers against decapentaplegic homolog 3	A, B	protein	125	Homo sapiens	P84022 (AlphaFold model)
DNA (5'-d(ptpgpcpapgpgpcpgpcpgpcpcptpgpcpa)-3')	C, D	DNA	16	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6ZMN_1 Mothers against decapentaplegic homolog 3 (chains A, B)
GPAVKRLLGWKQGDEEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSL
DGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVE
TPVLP

Sequence of entity 2 (C, D), FASTA

>6ZMN_2 DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3') (chains C, D)
TGCAGGCGCGCCTGCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (ACT, EDO, PGE) are not listed.

Primary citation

Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes. Ruiz, L., Kaczmarska, Z., Gomes, T. et al. Comput Struct Biotechnol J (2021) 19:632-646. DOI 10.1016/j.csbj.2020.12.044 · 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.
5ODG 2.12 Å, Crystal structure of Smad3-MH1 bound to the GGCT 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…

Browse structure collections

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