1LXI | pdb_00001lxi

Refinement of BMP7 crystal structure

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1lxia_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	Transforming growth factor (TGF)-beta	Bone morphogenetic protein-7 (BMP-7)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Transforming growth factor (TGF)-beta	8020226	4003433	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cystine-knot cytokines	8032606	3000846	SCOP2 (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		e1lxiA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: EGF_CA	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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
A	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	BONE MORPHOGENETIC PROTEIN 7	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding BMP receptor binding receptor serine/threonine kinase binding signaling receptor binding transmembrane receptor protein serine/threonine kinase binding cytokine activity heparin binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding BMP receptor binding receptor serine/threonine kinase binding signaling receptor binding transmembrane receptor protein serine/threonine kinase binding cytokine activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound 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 regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process 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 regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis neuron differentiation cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway 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 signaling cell surface receptor signaling pathway 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 regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling heart development circulatory system development embryonic epithelial tube formation chordate embryonic development neural fold formation tube formation embryo development epithelial tube formation primary neural tube formation tube morphogenesis neural fold elevation formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of an epithelial fold morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue morphogenesis anatomical structure morphogenesis neural tube formation anatomical structure formation involved in morphogenesis head development brain development central nervous system development hindbrain development epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process regulation of multicellular organismal development positive regulation of epithelial cell differentiation extraembryonic membrane development allantois development branching morphogenesis of an epithelial tube morphogenesis of a branching structure morphogenesis of a branching epithelium renal system development kidney vasculature development negative regulation of cell proliferation involved in kidney development renal system vasculature development regulation of glomerular mesangial cell proliferation negative regulation of glomerular mesangial cell proliferation nephron development blood vessel development negative regulation of cell population proliferation cell population proliferation cell proliferation involved in kidney development glomerular mesangium development vasculature development glomerulus development regulation of cell population proliferation glomerular mesangial cell proliferation glomerulus vasculature development kidney development negative regulation of mesenchymal cell apoptotic process regulation of somatic stem cell population maintenance regulation of programmed cell death stem cell population maintenance negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis mesenchymal cell apoptotic process involved in nephron morphogenesis somatic stem cell population maintenance animal organ morphogenesis negative regulation of programmed cell death regulation of apoptotic process regulation of mesenchymal cell apoptotic process regulation of stem cell population maintenance cell death negative regulation of stem cell population maintenance negative regulation of apoptotic process involved in development negative regulation of apoptotic process negative regulation of somatic stem cell population maintenance maintenance of cell number negative regulation of multicellular organismal process apoptotic process involved in morphogenesis nephron morphogenesis apoptotic process involved in development negative regulation of apoptotic process involved in morphogenesis mesenchymal cell apoptotic process regulation of apoptotic process involved in development kidney morphogenesis mesenchymal stem cell maintenance involved in nephron morphogenesis apoptotic process programmed cell death positive regulation of locomotion regulation of cell motility heart morphogenesis cardiac neural crest cell development involved in heart development neural crest cell development mesenchyme development mesenchymal cell migration positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis positive regulation of cell migration cell migration neural crest cell migration neural crest cell differentiation stem cell differentiation cardiac neural crest cell differentiation involved in heart development regulation of locomotion outflow tract morphogenesis cardiac neural crest cell migration involved in outflow tract morphogenesis cell development ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell motility locomotion stem cell development cardiac neural crest cell development involved in outflow tract morphogenesis cell migration involved in heart development cardiocyte differentiation regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis mesenchymal cell differentiation 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 response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus mesonephros development negative regulation of cell cycle cell cycle regulation of cell cycle positive regulation of programmed cell death positive regulation of apoptotic process mesenchyme morphogenesis nephrogenic mesenchyme development kidney mesenchyme development nephrogenic mesenchyme morphogenesis kidney mesenchyme morphogenesis regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of biomineral tissue development ossification biomineral tissue development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification endocardial cushion morphogenesis endocardial cushion formation endocardial cushion development kidney mesenchymal cell proliferation metanephric mesenchyme development metanephric mesenchymal cell proliferation involved in metanephros development metanephros development cell proliferation involved in metanephros development mesenchymal cell proliferation monocyte aggregation cell adhesion cell-cell adhesion leukocyte cell-cell adhesion leukocyte aggregation pharyngeal system development cardiac chamber morphogenesis cardiac septum development cardiac septum morphogenesis cardiac chamber development placenta development chorio-allantoic fusion labyrinthine layer development in utero embryonic development embryonic placenta morphogenesis labyrinthine layer morphogenesis embryonic placenta development embryonic organ development epithelial to mesenchymal transition positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion heterotypic cell-cell adhesion positive regulation of heterotypic cell-cell adhesion regulation of cell-cell adhesion regulation of heterotypic cell-cell adhesion sensory organ development embryonic eye morphogenesis visual system development embryonic camera-type eye development eye morphogenesis sensory system development embryonic organ morphogenesis camera-type eye morphogenesis eye development embryonic camera-type eye morphogenesis sensory organ morphogenesis camera-type eye development cardiac muscle tissue development striated muscle tissue development muscle tissue development regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis negative regulation of nervous system development negative regulation of cell development pericardium morphogenesis morphogenesis of an epithelial sheet pericardium development 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II 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 formation of primary germ layer mesoderm morphogenesis gastrulation mesoderm formation mesoderm development negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process 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 response to hormone response to peptide hormone response to oxygen-containing compound response to nitrogen compound hyaluranon cable assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis cellular component organization cellular component assembly positive regulation of hyaluranon cable assembly cellular component organization or biogenesis regulation of hyaluranon cable assembly cellular response to oxidative stress detoxification regulation of cellular response to stress reactive oxygen species metabolic process cellular response to chemical stress regulation of cellular response to oxidative stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species regulation of response to stress regulation of response to oxidative stress cellular detoxification regulation of superoxide metabolic process cellular response to oxygen-containing compound response to reactive oxygen species regulation of removal of superoxide radicals response to toxic substance superoxide metabolic process removal of superoxide radicals response to oxidative stress regulation of response to reactive oxygen species cellular response to superoxide regulation of reactive oxygen species metabolic process cellular response to toxic substance response to oxygen radical embryonic skeletal joint development embryonic skeletal joint morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic skeletal system morphogenesis odontogenesis of dentin-containing tooth odontogenesis regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition heart trabecula morphogenesis trabecula morphogenesis regulation of reproductive process prostate gland epithelium morphogenesis gland morphogenesis reproductive structure development animal organ formation regulation of morphogenesis of a branching structure regulation of animal organ morphogenesis prostatic bud formation urogenital system development prostate gland morphogenesis prostate gland development reproductive process gland development lateral sprouting from an epithelium developmental process involved in reproduction negative regulation of prostatic bud formation regulation of morphogenesis of an epithelium morphogenesis of an epithelial bud regulation of anatomical structure morphogenesis reproductive system development regulation of prostatic bud formation negative regulation of reproductive process regulation of animal organ formation negative regulation of morphogenesis of an epithelium limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis plasma membrane bounded cell projection organization neuron development negative regulation of signaling negative regulation of cell communication negative regulation of response to stimulus negative regulation of signal transduction Notch signaling pathway negative regulation of Notch signaling pathway regulation of Notch signaling pathway metanephric mesenchyme morphogenesis muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process ureteric bud development mesonephric epithelium development kidney epithelium development mesonephric tubule development dendrite development positive regulation of neuron differentiation axonogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance regulation of osteoblast differentiation positive regulation of osteoblast differentiation fat cell differentiation positive regulation of brown fat cell differentiation positive regulation of fat cell differentiation regulation of brown fat cell differentiation brown fat cell differentiation regulation of fat cell differentiation response to nutrient levels response to vitamin D response to lipid response to nutrient response to vitamin regulation of neuron projection development positive regulation of neuron projection development positive regulation of cell projection organization regulation of cell projection organization positive regulation of dendrite development regulation of dendrite development regulation of plasma membrane bounded cell projection organization negative regulation of intracellular signal transduction regulation of non-canonical NF-kappaB signal transduction negative regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction embryonic pattern specification pattern specification process branching involved in salivary gland morphogenesis salivary gland development salivary gland morphogenesis exocrine system development regulation of mitotic nuclear division mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle cell cycle process mitotic nuclear division negative regulation of cellular component organization regulation of cell cycle process organelle fission negative regulation of cell cycle process regulation of organelle organization organelle organization nuclear division mitotic cell cycle process negative regulation of nuclear division negative regulation of organelle organization regulation of nuclear division negative regulation of mitotic nuclear division regulation of branching involved in prostate gland morphogenesis branching involved in prostate gland morphogenesis ameloblast differentiation columnar/cuboidal epithelial cell differentiation response to estradiol	cellular anatomical structure extracellular region extracellular space membrane-bounded organelle organelle vesicle cell periphery extracellular matrix external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P18075	prostate cancer pulmonary fibrosis endometriosis Liver Cirrhosis, Experimental interstitial cystitis major depressive disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor bone resorption disease gastric neoplasm hereditary diffuse gastric adenocarcinoma malignant ependymoma non-small cell lung carcinoma ovarian cancer prostate cancer pulmonary fibrosis endometriosis Liver Cirrhosis, Experimental interstitial cystitis major depressive disorder medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor bone resorption disease gastric neoplasm hereditary diffuse gastric adenocarcinoma malignant ependymoma non-small cell lung carcinoma ovarian cancer bone fracture coloboma cutaneous lupus erythematosus esophageal adenocarcinoma glioblastoma idiopathic interstitial pneumonia lung cancer oligodendroglioma pilocytic astrocytoma psoriasis colorectal cancer gastric cancer

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.