5NB8 | pdb_00005nb8

Structure of vWC domain from CCN3

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Beta-lactamase2	e5nb8D1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: Beta-lactamase2	ECOD (v294.1)
C	Beta-lactamase2	e5nb8C1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: Beta-lactamase2	ECOD (v294.1)
B	Beta-lactamase2	e5nb8B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: Beta-lactamase2	ECOD (v294.1)
A	UCR_6-4kD	e5nb8A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: The swivelling beta/beta/alpha domain	T: The swivelling beta/beta/alpha domain	F: UCR_6-4kD	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00093	von Willebrand factor type C domain (VWC)	von Willebrand factor type C domain	The high cutoff was used to prevent overlap with Pfam:PF00094.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Protein NOV homolog	protein binding binding signaling receptor binding Notch binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cell adhesion molecule binding protein-containing complex binding integrin binding hormone activity protein binding binding signaling receptor binding Notch binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cell adhesion molecule binding protein-containing complex binding integrin binding hormone activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	muscle cell migration cell migration cellular process cell motility smooth muscle cell migration cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion negative regulation of leukocyte chemotaxis regulation of cell motility regulation of cellular process response to stimulus regulation of response to external stimulus negative regulation of biological process muscle cell migration cell migration cellular process cell motility smooth muscle cell migration cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion negative regulation of leukocyte chemotaxis regulation of cell motility regulation of cellular process response to stimulus regulation of response to external stimulus negative regulation of biological process negative regulation of chemotaxis negative regulation of monocyte chemotaxis regulation of monocyte chemotaxis taxis negative regulation of cellular process regulation of cell migration myeloid leukocyte migration regulation of immune system process regulation of mononuclear cell migration negative regulation of cell migration locomotion cell chemotaxis chemotaxis regulation of biological process regulation of leukocyte chemotaxis negative regulation of response to stimulus regulation of leukocyte migration biological regulation response to external stimulus regulation of chemotaxis monocyte chemotaxis leukocyte migration cellular response to chemical stimulus negative regulation of leukocyte migration negative regulation of immune system process regulation of response to stimulus immune system process regulation of locomotion response to chemical negative regulation of response to external stimulus mononuclear cell migration negative regulation of cell motility leukocyte chemotaxis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis ameboidal-type cell migration fibroblast migration developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation positive regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway negative regulation of signaling signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of intracellular signal transduction regulation of signal transduction negative regulation of cell communication intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of signal transduction SMAD protein signal transduction regulation of cell communication regulation of SMAD protein signal transduction negative regulation of SMAD protein signal transduction negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cell population proliferation type B pancreatic cell proliferation epithelial cell proliferation system process negative regulation of nervous system process nervous system process regulation of system process sensory perception of pain regulation of nervous system process sensory perception regulation of sensory perception regulation of multicellular organismal process regulation of sensory perception of pain negative regulation of multicellular organismal process negative regulation of sensory perception of pain multicellular organismal-level homeostasis homeostatic process hematopoietic stem cell homeostasis homeostasis of number of cells cell adhesion connective tissue development tissue development skeletal system development chondrocyte differentiation cartilage development negative regulation of cell population proliferation negative regulation of chondrocyte proliferation regulation of cell population proliferation chondrocyte proliferation 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 endothelial cell migration endothelial cell chemotaxis muscle cell proliferation smooth muscle cell proliferation regulation of defense response negative regulation of inflammatory response defense response regulation of inflammatory response response to stress regulation of response to stress negative regulation of defense response inflammatory response cell-cell adhesion epithelial cell-cell adhesion endothelial cell-cell adhesion cell adhesion mediated by integrin negative regulation of protein transport regulation of localization establishment of protein localization nitrogen compound transport negative regulation of transport localization negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell intracellular protein localization regulation of biological quality regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion establishment of localization regulation of protein secretion regulation of secretion negative regulation of protein secretion regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport hormone secretion protein localization to extracellular region negative regulation of peptide secretion peptide secretion regulation of secretion by cell secretion by cell signal release negative regulation of protein localization regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport peptide transport negative regulation of insulin secretion protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion negative regulation of muscle cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation myotube differentiation muscle structure development negative regulation of myotube differentiation regulation of myotube differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of striated muscle cell differentiation regulation of muscle cell differentiation striated muscle cell differentiation tissue regeneration developmental growth bone regeneration regeneration ossification positive regulation of multicellular organismal process positive regulation of ossification regulation of ossification positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway positive regulation of signaling regulation of non-canonical NF-kappaB signal transduction negative regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell body neuronal cell body axon cell-cell junction cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell body neuronal cell body axon cell-cell junction anchoring junction gap junction cell junction extracellular matrix external encapsulating structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000867	Insulin-like growth factor-binding protein, IGFBP	Domain
A, B, C, D	IPR043973	CCN, TSP1 domain	Domain
A, B, C, D	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
A, B, C, D	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
A, B, C, D	IPR006208	Glycoprotein hormone subunit beta	Domain
A, B, C, D	IPR012395	IGFBP-related, CNN	Family
A, B, C, D	IPR001007	VWFC domain	Domain
A, B, C, D	IPR050941	Cellular Communication Network Factor	Family
A, B, C, D	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A, B, C, D	IPR006207	Cystine knot, C-terminal	Domain
A, B, C, D	IPR017891	Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site	Conserved Site

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.