3L8I

Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DUF1241_N	e3l8iA1	A: alpha arrays	X: CCM3/GCKIII dimerization domain (From Topology)	H: CCM3/GCKIII dimerization domain (From Topology)	T: CCM3/GCKIII dimerization domain	F: DUF1241_N	ECOD (1.6)
A	DUF1241_C	e3l8iA2	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: DUF1241_C	ECOD (1.6)
B	DUF1241_N	e3l8iB1	A: alpha arrays	X: CCM3/GCKIII dimerization domain (From Topology)	H: CCM3/GCKIII dimerization domain (From Topology)	T: CCM3/GCKIII dimerization domain	F: DUF1241_N	ECOD (1.6)
B	DUF1241_C	e3l8iB2	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: DUF1241_C	ECOD (1.6)
D	DUF1241_N	e3l8iD1	A: alpha arrays	X: CCM3/GCKIII dimerization domain (From Topology)	H: CCM3/GCKIII dimerization domain (From Topology)	T: CCM3/GCKIII dimerization domain	F: DUF1241_N	ECOD (1.6)
D	DUF1241_C	e3l8iD2	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: DUF1241_C	ECOD (1.6)
C	DUF1241_N	e3l8iC2	A: alpha arrays	X: CCM3/GCKIII dimerization domain (From Topology)	H: CCM3/GCKIII dimerization domain (From Topology)	T: CCM3/GCKIII dimerization domain	F: DUF1241_N	ECOD (1.6)
C	DUF1241_C	e3l8iC1	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: DUF1241_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.12.70	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
A	1.20.120.330	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nucleotidyltransferases domain 2	CATH (4.3.0)
B	1.10.12.70	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
B	1.20.120.330	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nucleotidyltransferases domain 2	CATH (4.3.0)
D	1.10.12.70	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
D	1.20.120.330	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Nucleotidyltransferases domain 2	CATH (4.3.0)
C	1.20.120.1950	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF20929	Programmed cell death protein 10, dimerisation domain (PDCD10_N)	Programmed cell death protein 10, dimerisation domain	Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration [1]. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability [ ...	Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration [1]. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability [2]. This protein plays an essential role in early embryonic angiogenesis and cardiovascular development [6]. PDCD10/CCM3 interacts with a variety of proteins, including paxillin, membrane receptor vascular epidermal growth factor receptor 2, CCM complex component CCM2 and germinal center kinase III proteins (GCKIII). It consists of a N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain (Pfam:PF06840) [3]. This entry represents the N-terminal dimerisation domain, consisting of four alpha-helices [3,4,5,6]. This domain is also found at the C-terminal of GCKIIIs (STK24/MST3, STK25, STK26/MST4), which adopts a closely related fold. GCKIIIs are involved in the regulation of apoptosis, cell proliferation, polarity, migration, and cytoskeleton remodelling. This domain mediates homo and heterodimerisation [5,6]. PDCD10/CCM3 forms a heterodimer with GCKIIIs analogous to CCM3 homodimer.	Domain
A, B, C, D	PF06840	Programmed cell death protein 10, C-terminal (PDC10_C)	Programmed cell death protein 10, C-terminal	Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration [1]. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability [ ...	Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration [1]. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability [2]. PDCD10/CCM3 contains an N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain (represented in this entry) [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Programmed cell death protein 10	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding	Golgi localization establishment of organelle localization localization cellular localization establishment of Golgi localization organelle localization establishment of localization in cell cellular process establishment of localization developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process Golgi localization establishment of organelle localization localization cellular localization establishment of Golgi localization organelle localization establishment of localization in cell cellular process establishment of localization developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of cellular response to stress positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette signal transduction positive regulation of stress-activated protein kinase signaling cascade positive regulation of cellular process regulation of signaling positive regulation of stress-activated MAPK cascade positive regulation of MAPK cascade regulation of stress-activated protein kinase signaling cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling regulation of protein stability regulation of biological quality protein stabilization negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic 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 metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification regulation of primary metabolic process regulation of nitrogen compound metabolic process positive regulation of protein modification process peptidyl-serine phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification nitrogen compound metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of peptidyl-serine phosphorylation positive regulation of nitrogen compound metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation Golgi inheritance organelle inheritance Golgi reassembly cellular component organization cellular component biogenesis organelle organization cellular component assembly cellular component organization or biogenesis Golgi organization endomembrane system organization cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation regulation of catalytic activity regulation of transferase activity regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of MAP kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity positive regulation of molecular function positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity intrinsic apoptotic signaling pathway in response to oxidative stress programmed cell death in response to reactive oxygen species cellular response to oxidative stress cellular response to chemical stress cellular response to reactive oxygen species hydrogen peroxide-mediated programmed cell death intrinsic apoptotic signaling pathway response to oxygen-containing compound intrinsic apoptotic signaling pathway in response to hydrogen peroxide cellular response to oxygen-containing compound response to reactive oxygen species apoptotic signaling pathway response to oxidative stress cellular response to chemical stimulus response to chemical regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis endothelial cell proliferation negative regulation of endothelial cell proliferation epithelial cell proliferation negative regulation of cell population proliferation negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis blood vessel endothelial cell proliferation involved in sprouting angiogenesis sprouting angiogenesis regulation of endothelial cell proliferation regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation epithelium development endothelium development tissue development positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion negative regulation of locomotion cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration tissue migration negative regulation of epithelial cell migration blood vessel endothelial cell migration negative regulation of cell migration regulation of cell migration involved in sprouting angiogenesis epithelium migration negative regulation of cell motility negative regulation of multicellular organismal process negative regulation of cell migration involved in sprouting angiogenesis ameboidal-type cell migration regulation of endothelial cell migration epithelial cell migration regulation of epithelial cell migration cell surface receptor signaling pathway Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway negative regulation of cellular metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process wound healing morphogenesis of an epithelium epiboly involved in wound healing morphogenesis of an epithelial sheet tissue morphogenesis epiboly wound healing, spreading of cells response to wounding protein localization regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of protein transport cellular macromolecule localization positive regulation of intracellular transport regulation of intracellular transport regulation of transport organic substance transport regulation of establishment of protein localization intracellular transport regulation of protein transport positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of cellular component organization regulation of organelle organization regulation of Golgi organization response to organic substance response to cytokine response to leukemia inhibitory factor cellular response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to organic substance	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane intracellular organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system Golgi membrane bounding membrane of organelle organelle membrane FAR/SIN/STRIPAK complex protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009652	Programmed cell death protein 10	Family
A, B, C, D	IPR046409	Programmed cell death protein 10, dimerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR048288	Programmed cell death protein 10, dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9BUL8	cerebral cavernous malformation 3 cerebrovascular disorder cavernous hemangioma famililal cerebral cavernous malformations lung cancer psoriasis cerebral cavernous malformation cerebrocostomandibular syndrome hereditary spastic paraplegia lymphoplasmacytic lymphoma cerebral cavernous malformation 1 intellectual disability plasma cell myeloma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.