3KMP | pdb_00003kmp

Crystal Structure of SMAD1-MH1/DNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3kmpa_	Alpha and beta proteins (a+b)	SMAD MH1 domain	SMAD MH1 domain	SMAD MH1 domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3kmpb_	Alpha and beta proteins (a+b)	SMAD MH1 domain	SMAD MH1 domain	SMAD MH1 domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SMAD MH1 domain	8083635	4002374	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SMAD MH1 domain	8083636	3001158	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SMAD MH1 domain	8083636	3001158	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	MH1	e3kmpA1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: MH1	ECOD (1.6)
B	MH1	e3kmpB1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: MH1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.520.10	Alpha Beta	Alpha-Beta Complex	Smad3	Chain A	CATH (4.3.0)
B	3.90.520.10	Alpha Beta	Alpha-Beta Complex	Smad3	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03165	MH1 domain (MH1)	MH1 domain	The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved ...	The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [1,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	5'-D(PAPTPCPAPGPTPCPTPAPGPAPCPAPTP*A)-3'	-	-	-
D	5'-D(PGPTPAPTPGPTPCPTPAPGPAPCPTPGP*A)-3'	-	-	-
A, B	SMAD1-MH1	co-SMAD binding SMAD binding protein binding binding RNA binding primary miRNA binding nucleic acid binding sequence-specific DNA binding DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity I-SMAD binding enzyme binding co-SMAD binding SMAD binding protein binding binding RNA binding primary miRNA binding nucleic acid binding sequence-specific DNA binding DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity I-SMAD binding enzyme binding DEAD/H-box RNA helicase binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding ion binding metal ion binding small molecule binding identical protein binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding kinase binding protein kinase binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis head development brain development nervous system development central nervous system development hindbrain development heart development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth striated muscle tissue development circulatory system development muscle cell proliferation cellular process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process bone development regulation of developmental process cellular developmental process negative regulation of developmental process negative regulation of biological process negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation negative regulation of cellular process negative regulation of cell differentiation RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of DNA-templated transcription positive regulation of miRNA transcription positive regulation of miRNA metabolic process regulation of primary metabolic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription cellular response to stimulus response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade signal transduction transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway regulation of cartilage development regulation of multicellular organismal development positive regulation of developmental process positive regulation of multicellular organismal process positive regulation of cartilage development regulation of multicellular organismal process midbrain development ossification osteoblast differentiation cellular response to BMP stimulus response to BMP BMP signaling pathway sexual reproduction reproductive process multicellular organismal reproductive process gamete generation osteoblast fate commitment cell fate commitment formation of primary germ layer mesodermal cell differentiation mesoderm morphogenesis embryonic morphogenesis embryo development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis tissue morphogenesis anatomical structure formation involved in morphogenesis mesodermal cell fate commitment mesoderm formation mesoderm development ureteric bud development mesonephric epithelium development epithelium development kidney epithelium development mesonephros development tube development renal system development kidney development mesonephric tubule development SMAD protein signal transduction negative regulation of cell population proliferation regulation of cell population proliferation regulation of osteoblast differentiation positive regulation of osteoblast differentiation positive regulation of cell differentiation regulation of sprouting angiogenesis angiogenesis regulation of vasculature development tube morphogenesis positive regulation of sprouting angiogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis positive regulation of angiogenesis sprouting angiogenesis vasculature development positive regulation of vasculature development regulation of angiogenesis defense response response to stress inflammatory response embryonic pattern specification pattern specification process stem cell differentiation	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus heteromeric SMAD protein complex nuclear protein-containing complex intracellular membrane-bounded organelle SMAD protein complex organelle inner membrane nuclear membrane membrane endomembrane system organelle envelope nuclear inner membrane nuclear envelope organelle membrane male germ cell nucleus germ cell nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen homomeric SMAD protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036578	SMAD MH1 domain superfamily	Homologous Superfamily
A, B	IPR017855	SMAD-like domain superfamily	Homologous Superfamily
A, B	IPR013019	MAD homology, MH1	Domain
A, B	IPR013790	Dwarfin	Family
A, B	IPR003619	MAD homology 1, Dwarfin-type	Domain
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR001132	SMAD domain, Dwarfin-type	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.