4YCG | pdb_00004ycg

Pro-bone morphogenetic protein 9

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cystine-knot cytokines	8070319	3000846	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cystine-knot cytokines	8070319	3000846	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	pro-TGF beta-like	8089962	3002405	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	pro-TGF beta-like	8089962	3002405	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)
D	Flavodoxin_2	e4ycgD1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)
C	Nop10p	e4ycgC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Nop10p	ECOD (v294.1)
B	Nop10p	e4ycgB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Nop10p	ECOD (v294.1)
A	VipB_2	e4ycgA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: VipB_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
C	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Bone Morphogenetic Protein 9 Prodomain	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine activity	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 cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling cellular developmental process ossification cell differentiation osteoblast differentiation cellular response to BMP stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway regulation of developmental process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process epithelium development regulation of multicellular organismal development positive regulation of epithelial cell differentiation blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular component organization or biogenesis activin receptor signaling pathway positive regulation of BMP signaling pathway regulation of BMP signaling pathway regulation of cellular response to growth factor stimulus positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process interleukin-8 production regulation of macromolecule metabolic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production branching morphogenesis of an epithelial tube epithelial tube morphogenesis morphogenesis of an epithelium branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration negative regulation of cell motility blood vessel endothelial cell migration cell migration cell motility locomotion negative regulation of cell migration vasculogenesis regulation of vasculature development regulation of anatomical structure morphogenesis positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis endothelium development positive regulation of endothelial cell differentiation endothelial cell differentiation regulation of endothelial cell differentiation positive regulation of DNA-templated transcription regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development negative regulation of multicellular organismal process Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II bicellular tight junction assembly positive regulation of cellular component organization tight junction organization cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly positive regulation of cellular component biogenesis regulation of cellular component biogenesis apical junction assembly regulation of cell junction assembly positive regulation of cell junction assembly positive regulation of bicellular tight junction assembly cell junction organization tight junction assembly negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA replication negative regulation of metabolic process DNA metabolic process DNA replication negative regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA replication negative regulation of cell population proliferation negative regulation of endothelial cell proliferation negative regulation of epithelial cell proliferation regulation of cartilage development positive regulation of cartilage development	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle
A, B	Bone Morphogenetic Protein 9 Growth Factor Domain	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine activity enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	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 cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process 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 cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling developmental process multicellular organismal process cellular developmental process ossification cell differentiation osteoblast differentiation cellular response to BMP stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway regulation of developmental process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process multicellular organism development positive regulation of cell differentiation anatomical structure development regulation of multicellular organismal process epithelium development regulation of multicellular organismal development positive regulation of epithelial cell differentiation tissue development blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development system development regulation of biosynthetic 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 regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular component organization or biogenesis activin receptor signaling pathway nervous system development generation of neurons neurogenesis neuron differentiation monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process small molecule metabolic process primary metabolic process glucose metabolic process positive regulation of BMP signaling pathway regulation of BMP signaling pathway regulation of cellular response to growth factor stimulus positive regulation of interleukin-8 production cytokine production regulation of cytokine production interleukin-8 production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production branching morphogenesis of an epithelial tube epithelial tube morphogenesis morphogenesis of an epithelium branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium vasculogenesis regulation of vasculature development regulation of anatomical structure morphogenesis positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis endothelium development positive regulation of endothelial cell differentiation endothelial cell differentiation regulation of endothelial cell differentiation negative regulation of locomotion regulation of cell motility endothelial cell migration negative regulation of endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II bicellular tight junction assembly positive regulation of cellular component organization tight junction organization cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly cell-cell junction organization regulation of bicellular tight junction assembly positive regulation of cellular component biogenesis regulation of cellular component biogenesis apical junction assembly regulation of cell junction assembly positive regulation of cell junction assembly positive regulation of bicellular tight junction assembly cell junction organization tight junction assembly negative regulation of cell population proliferation negative regulation of endothelial cell proliferation negative regulation of epithelial cell proliferation regulation of cartilage development connective tissue development animal organ development skeletal system development positive regulation of cartilage development cartilage development	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR029034	Cystine-knot cytokine	Homologous Superfamily
C, D	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
C, D	IPR015615	Transforming growth factor-beta-like	Family
C, D	IPR001111	TGF-beta, propeptide	Domain
C, D	IPR001839	Transforming growth factor-beta, C-terminal	Domain
A, B	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
A, B	IPR015615	Transforming growth factor-beta-like	Family
A, B	IPR001111	TGF-beta, propeptide	Domain
A, B	IPR001839	Transforming growth factor-beta, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q9UK05	hereditary hemorrhagic telangiectasia telangiectasia, hereditary hemorrhagic, type 5 pulmonary hypertension arteriovenous hemangioma/malformation Fracture pulmonary arterial hypertension bone fracture idiopathic pulmonary arterial hypertension cerebrovascular disorder hepatocellular carcinoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.