3U7D | pdb_00003u7d

Crystal structure of the KRIT1/CCM1 FERM domain in complex with the heart of glass (HEG1) cytoplasmic tail

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)
C	FERM_C_CCM1	e3u7dC9	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_CCM1	ECOD (1.6)
C	FERM_M	e3u7dC7	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
C	KOG4335	e3u7dC8	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4335	ECOD (1.6)
A	FERM_C_CCM1	e3u7dA5	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_CCM1	ECOD (1.6)
A	FERM_M	e3u7dA4	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
A	KOG4335	e3u7dA6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4335	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
C	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF24522	KRIT1/FRMD8, FERM domain C-lobe (KRIT1_FRMD8_FERM_C)	KRIT1/FRMD8, FERM domain C-lobe	KRIT1, also known as CCM1, a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins [1]. Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of protei ...	KRIT1, also known as CCM1, a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins [1]. Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of proteins whose mutations are found in cerebral cavernous malformations, characterised by cerebral hemorrhages and vascular malformations in the central nervous system. KRIT1 localization is mediated by its FERM domain [2]. This entry represents the FERM domain C-lobe. This entry also includes the paralogue of KRIT1, FRMD8, a protein that promotes the cell surface stability of iRhom1/RHBDF1 and iRhom2/RHBDF2 and prevents their degradation via the endolysosomal pathway. By acting on iRhoms, FRMD8 is involved in ADAM17-mediated shedding of TNF, amphiregulin/AREG, HBEGF and TGFA from the cell surface [3,4].	Domain
A, C	PF00373	FERM central domain (FERM_M)	FERM central domain	This domain is the central structural domain of the FERM domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Protein HEG homolog 1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding	developmental process heart development multicellular organismal process cardiac atrium morphogenesis cardiac chamber morphogenesis heart morphogenesis animal organ development cardiac atrium development circulatory system development multicellular organism development anatomical structure morphogenesis anatomical structure development cardiac chamber development animal organ morphogenesis developmental process heart development multicellular organismal process cardiac atrium morphogenesis cardiac chamber morphogenesis heart morphogenesis animal organ development cardiac atrium development circulatory system development multicellular organism development anatomical structure morphogenesis anatomical structure development cardiac chamber development animal organ morphogenesis system development regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of fibroblast growth factor production positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process positive regulation of fibroblast growth factor production fibroblast growth factor production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process epithelium development tissue development pericardium development venous blood vessel development blood vessel morphogenesis tube development venous blood vessel morphogenesis vasculature development tube morphogenesis blood vessel development endothelial cell differentiation cellular developmental process endothelium development cell development epithelial cell differentiation cell morphogenesis endothelial cell development epithelial cell development endothelial cell morphogenesis epithelial cell morphogenesis cell differentiation regulation of body fluid levels regulation of biological quality ventricular septum development cardiac septum development cardiac ventricle development negative regulation of membrane permeability regulation of membrane permeability respiratory tube development lung development respiratory system development heart growth developmental growth cardiac muscle tissue development growth organ growth striated muscle tissue development cardiac muscle tissue growth muscle tissue development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development cellular response to stimulus small GTPase-mediated signal transduction negative regulation of Rho protein signal transduction response to stimulus signaling negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction Rho protein signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of small GTPase mediated signal transduction regulation of Rho protein signal transduction negative regulation of signal transduction regulation of response to stimulus regulation of cell communication system process lymph circulation circulatory system process vasculogenesis localization macromolecule localization intracellular protein localization protein localization to cell junction multicellular organism growth post-embryonic development lymph vessel development cellular component organization cell junction organization cellular component organization or biogenesis cell-cell junction organization ventricular cardiac muscle tissue morphogenesis muscle structure development ventricular cardiac muscle tissue development ventricular trabecula myocardium morphogenesis muscle organ development muscle tissue morphogenesis tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis trabecula morphogenesis muscle organ morphogenesis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction extracellular region
A, C	Krev interaction trapped protein 1	ion binding binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding cytoskeletal protein binding microtubule binding protein binding tubulin binding ion binding binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding cytoskeletal protein binding microtubule binding protein binding tubulin binding GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity	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 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 component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process integrin activation cellular component organization or biogenesis cell redox homeostasis cellular homeostasis homeostatic process epithelium development endothelium development tissue development negative regulation of locomotion regulation of cell motility regulation of cellular process endothelial cell migration negative regulation of biological process negative regulation of endothelial cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process regulation of endothelial cell migration negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development negative regulation of multicellular organismal process negative regulation of endothelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation negative regulation of endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette signal transduction	cell-cell junction cellular anatomical structure anchoring junction cell junction cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex intracellular organelle cytoskeleton organelle membraneless organelle cell-cell junction cellular anatomical structure anchoring junction cell junction cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
B, D	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B, D	IPR000742	EGF-like domain	Domain
B, D	IPR001881	EGF-like calcium-binding domain	Domain
B, D	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A, C	IPR041791	Krev interaction trapped protein 1, FERM domain C-lobe	Domain
A, C	IPR000299	FERM domain	Domain
A, C	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A, C	IPR043058	KRIT, N-terminal NPxY motif-rich domain superfamily	Homologous Superfamily
A, C	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, C	IPR019748	FERM central domain	Domain
A, C	IPR056485	KRIT1, ARM-repeats domain	Domain
A, C	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, C	IPR002110	Ankyrin repeat	Repeat
A, C	IPR019749	Band 4.1 domain	Domain
A, C	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A, C	IPR032022	KRIT, N-terminal NPxY motif-rich region	Domain
A, C	IPR057096	KRIT1/FRMD8, FERM domain C-lobe	Domain
A, C	IPR051594	KRIT1/FRMD8	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q9ULI3	astrocytic tumor glioblastoma lung adenocarcinoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm transitional cell carcinoma cystic fibrosis interstitial cystitis lung cancer medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis gastric carcinoma astrocytic tumor glioblastoma lung adenocarcinoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm transitional cell carcinoma cystic fibrosis interstitial cystitis lung cancer medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis gastric carcinoma juvenile dermatomyositis lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma Sjogren syndrome
A, C	Pharos: O00522	Hemangioma, Cavernous, Central Nervous System cerebral cavernous malformation 1 cerebrovascular disorder famililal cerebral cavernous malformations cavernous hemangioma cerebral cavernous malformation cerebrocostomandibular syndrome intellectual disability hereditary hemorrhagic telangiectasia

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.