5VQF

Crystal Structure of pro-TGF-beta 1

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	pro-TGF beta-like	8089959	3002405	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cystine-knot cytokines	8089960	3000846	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	pro-TGF beta-like	8089959	3002405	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cystine-knot cytokines	8089960	3000846	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	pro-TGF beta-like	8089959	3002405	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cystine-knot cytokines	8089960	3000846	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cystine-knot cytokines	8089960	3000846	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	pro-TGF beta-like	8089959	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)
A	TGFb_propeptide	e5vqfA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: TGFb_propeptide	ECOD (1.6)
A	TGF_beta	e5vqfA2	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
B	TGFb_propeptide	e5vqfB1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: TGFb_propeptide	ECOD (1.6)
B	TGF_beta	e5vqfB2	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
C	TGFb_propeptide	e5vqfC1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: TGFb_propeptide	ECOD (1.6)
C	TGF_beta	e5vqfC2	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
D	TGFb_propeptide	e5vqfD2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: TGFb_propeptide	ECOD (1.6)
D	TGF_beta	e5vqfD1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.250.2330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	2.60.120.970	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	6.10.250.2330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	2.60.120.970	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.970	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.970	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00688	TGF-beta propeptide (TGFb_propeptide)	TGF-beta propeptide	-	Family
A, B, 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
A, B, C, D	Transforming growth factor beta-1	transforming growth factor beta receptor binding protein binding binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding type II transforming growth factor beta receptor binding transforming growth factor beta receptor binding protein binding binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding type II transforming growth factor beta receptor binding type III transforming growth factor beta receptor binding cytokine activity	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 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 gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development cellular metabolic process reactive oxygen species metabolic process regulation of superoxide metabolic process regulation of cellular metabolic process positive regulation of cellular metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation metabolic process positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport regulation of protein localization transport nuclear transport regulation of protein localization to nucleus localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus regulation of intracellular transport regulation of transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport intracellular protein transport immune system development lymph node development immune system process hematopoietic or lymphoid organ development response to ketone response to lipid response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound response to organic cyclic compound cellular biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cellular biosynthetic process positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis chemotaxis positive regulation of locomotion regulation of response to external stimulus response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to external stimulus taxis regulation of locomotion locomotion negative regulation of cellular process negative regulation of biological process negative regulation of cell cycle cell cycle regulation of cell cycle regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation response to sterol response to alcohol response to cholesterol regulation of growth growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death cell surface receptor protein tyrosine kinase signaling pathway positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway ERBB signaling pathway positive regulation of cell division cell division regulation of cell division positive regulation of nucleocytoplasmic transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport positive regulation of protein localization to nucleus positive regulation of protein import into nucleus positive regulation of transport positive regulation of protein localization positive regulation of intracellular protein transport regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion regulation of cell-cell adhesion 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 cell migration blood vessel endothelial cell migration regulation of endothelial cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration cellular developmental process cell differentiation mesenchyme development mesenchymal cell differentiation tissue development epithelial to mesenchymal transition response to stress response to wounding regulation of immune effector process negative regulation of macrophage cytokine production cytokine production regulation of immune system process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response immune response negative regulation of immune effector process negative regulation of cellular biosynthetic process immune effector process negative regulation of production of molecular mediator of immune response negative regulation of gene expression regulation of macrophage cytokine production negative regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response negative regulation of multicellular organismal process regulation of cytokine production regulation of multicellular organismal process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response negative regulation of cytokine production negative regulation of immune system process negative regulation of biosynthetic process macrophage cytokine production ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process small molecule metabolic process ribose phosphate biosynthetic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process connective tissue development skeletal system development chondrocyte differentiation cartilage development extracellular matrix organization extracellular matrix assembly extracellular structure organization external encapsulating structure organization negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of collagen metabolic process positive regulation of collagen biosynthetic process collagen metabolic process positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription mucopolysaccharide metabolic process carbohydrate derivative catabolic process catabolic process hyaluronan catabolic process glycosaminoglycan metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process hyaluronan metabolic process aminoglycan metabolic process cellular response to growth factor stimulus cellular response to transforming growth factor beta 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 cellular catabolic process receptor catabolic process receptor metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of RNA metabolic process fat cell differentiation regulation of developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation positive regulation of protein metabolic process regulation of muscle tissue development regulation of striated muscle tissue development striated muscle tissue development muscle structure development regulation of muscle organ development muscle tissue development muscle organ development positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition positive regulation of developmental process positive regulation of cell differentiation positive regulation of multicellular organismal process negative regulation of myoblast differentiation regulation of myoblast differentiation myoblast differentiation regulation of fibroblast migration positive regulation of fibroblast migration fibroblast migration positive regulation of cell migration ameboidal-type cell migration positive regulation of cell motility skeletal muscle tissue development regulation of skeletal muscle tissue development skeletal muscle organ development negative regulation of muscle organ development negative regulation of skeletal muscle tissue development negative regulation of muscle tissue development negative regulation of striated muscle tissue development positive regulation of cell population proliferation membrane protein intracellular domain proteolysis proteolysis membrane protein proteolysis positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration positive regulation of secretion by cell protein localization to extracellular region regulation of secretion by cell secretion by cell positive regulation of secretion secretion establishment of protein localization to extracellular region export from cell protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion epithelium development epithelial cell differentiation neuroepithelial cell differentiation odontoblast differentiation columnar/cuboidal epithelial cell differentiation interleukin-17 production regulation of interleukin-17 production positive regulation of interleukin-17 production positive regulation of cytokine production regulation of leukocyte differentiation positive regulation of nervous system development mononuclear cell differentiation regulation of neurogenesis regulation of cell development positive regulation of gliogenesis gliogenesis microglia differentiation regulation of macrophage differentiation positive regulation of immune system process regulation of microglia differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation nervous system development positive regulation of myeloid leukocyte differentiation positive regulation of macrophage differentiation central nervous system development positive regulation of microglia differentiation leukocyte differentiation myeloid leukocyte differentiation cell development regulation of gliogenesis regulation of nervous system development neurogenesis positive regulation of hemopoiesis positive regulation of neurogenesis regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation macrophage differentiation regulation of glial cell differentiation positive regulation of glial cell differentiation glial cell differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation defense response inflammatory response hematopoietic progenitor cell differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of immune response positive regulation of isotype switching to IgA isotypes positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response DNA recombination DNA metabolic process positive regulation of DNA metabolic process B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of DNA metabolic process immunoglobulin production positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response positive regulation of lymphocyte activation somatic recombination of immunoglobulin gene segments regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation positive regulation of isotype switching positive regulation of immune effector process positive regulation of immunoglobulin production regulation of isotype switching cell activation isotype switching to IgA isotypes somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation lymphocyte mediated immunity regulation of DNA recombination positive regulation of leukocyte mediated immunity cell activation involved in immune response positive regulation of cell activation positive regulation of leukocyte activation leukocyte mediated immunity somatic diversification of immune receptors positive regulation of adaptive immune response somatic recombination of immunoglobulin genes involved in immune response regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity regulation of immune response isotype switching immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of lymphocyte mediated immunity regulation of isotype switching to IgA isotypes lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte activation involved in immune response B cell activation immunoglobulin mediated immune response adaptive immune response positive regulation of B cell activation regulation of lymphocyte mediated immunity regulation of immunoglobulin production regulation of hyaluronan biosynthetic process regulation of polysaccharide metabolic process negative regulation of hyaluronan biosynthetic process polysaccharide metabolic process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan biosynthetic process regulation of carbohydrate biosynthetic process cell junction organization cell-cell junction organization response to estradiol	intracellular anatomical structure cytoplasm cellular anatomical entity extracellular region extracellular space cell surface cell periphery extracellular matrix external encapsulating structure blood microparticle membrane-bounded organelle intracellular organelle organelle nucleus intracellular anatomical structure cytoplasm cellular anatomical entity extracellular region extracellular space cell surface cell periphery extracellular matrix external encapsulating structure blood microparticle membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003939	Transforming growth factor beta-1 proprotein	Family
A, B, C, D	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A, B, C, D	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
A, B, C, D	IPR001839	Transforming growth factor-beta, C-terminal	Domain
A, B, C, D	IPR016319	Transforming growth factor-beta	Family
A, B, C, D	IPR015615	Transforming growth factor-beta-related	Family
A, B, C, D	IPR001111	TGF-beta, propeptide	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.