3W8I | pdb_00003w8i

Crystal structure of CCM3 in complex with the C-terminal regulatory domain of MST4

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)
B		e3w8iB1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: PEPCK_N	F:	ECOD (20:10:01)
A		e3w8iA2	A: cradle loop barrel	X: RIFT-related	H: double psi	T: Kunitz_BPTI	F:	ECOD (20:10:01)
A		e3w8iA1	A: cradle loop barrel	X: RIFT-related	H: double psi	T: BSH_CusB	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.12.70	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
A	1.20.120.1950	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
B	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	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
B	Serine/threonine-protein kinase MST4	catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding identical protein binding protein binding protein homodimerization activity protein dimerization activity protein serine/threonine kinase activity	regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of microvillus assembly positive regulation of biological process plasma membrane bounded cell projection assembly microvillus organization cellular component biogenesis cellular component organization regulation of microvillus assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization positive regulation of microvillus assembly positive regulation of biological process plasma membrane bounded cell projection assembly microvillus organization cellular component biogenesis cellular component organization regulation of microvillus assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process regulation of biological process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly regulation of microvillus organization microvillus assembly cellular process cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly apoptotic process cell death programmed cell death regulation of apoptotic process regulation of programmed cell death cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process cellular response to nutrient levels response to nutrient levels response to starvation cellular response to starvation negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion signaling signal transduction intracellular signal transduction cell communication	cellular anatomical structure membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical structure membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle Golgi-associated vesicle cytoplasm cytosol vesicle membrane organelle membrane Golgi apparatus endomembrane system perinuclear region of cytoplasm FAR/SIN/STRIPAK complex protein-containing complex
A	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 anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development 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 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 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 positive regulation of protein modification process peptidyl-serine phosphorylation phosphate-containing compound metabolic process peptidyl-amino acid modification protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process positive regulation of peptidyl-serine phosphorylation 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 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 regulation of endothelial cell migration blood vessel endothelial cell migration negative regulation of cell migration regulation of cell migration involved in sprouting angiogenesis negative regulation of cell motility negative regulation of cell migration involved in sprouting angiogenesis cell surface receptor signaling pathway Notch signaling pathway regulation of Notch signaling pathway positive regulation of Notch signaling pathway negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic 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 regulation of localization establishment of protein localization regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport intracellular protein localization regulation of intracellular transport regulation of 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 response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space 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
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR046409	Programmed cell death protein 10, dimerisation domain superfamily	Homologous Superfamily
B	IPR000719	Protein kinase domain	Domain
B	IPR050629	STE20/SPS1-related Proline-Alanine-rich Kinase	Family
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR048288	Programmed cell death protein 10, dimerisation domain	Domain
B	IPR035056	MST4, kinase domain	Domain
A	IPR009652	Programmed cell death protein 10	Family
A	IPR046409	Programmed cell death protein 10, dimerisation domain superfamily	Homologous Superfamily
A	IPR048288	Programmed cell death protein 10, dimerisation domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9P289	plasma cell myeloma adenoma gastric adenocarcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis HER2-positive carcinoma of breast lung cancer malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer plasma cell myeloma adenoma gastric adenocarcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cystic fibrosis HER2-positive carcinoma of breast lung cancer malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung carcinoma malignant mesothelioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm
A	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 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.