4HDQ

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the Heart of Glass (HEG1) cytoplasmic tail

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (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	FERM_C_CCM1	e4hdqA5	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	e4hdqA4	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	e4hdqA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4335	ECOD (1.6)
B	Ras	e4hdqB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00373	FERM central domain (FERM_M)	FERM central domain	This domain is the central structural domain of the FERM domain.	Domain
B	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Krev interaction trapped protein 1	binding ion 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 binding ion 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 multicellular organism development anatomical structure morphogenesis 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 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 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 anchoring junction cell junction cellular anatomical entity cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle cell-cell junction anchoring junction cell junction cellular anatomical entity cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle extracellular region extracellular space
B	Ras-related protein Rap-1b	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding protein-containing complex binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling regulation of biological process neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular response to stimulus small GTPase-mediated signal transduction response to stimulus intracellular signal transduction intracellular signaling cassette signal transduction Rap protein signal transduction calcium-ion regulated exocytosis positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of cellular process positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling cell population proliferation cellular response to nitrogen compound response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP response to organic cyclic compound regulation of calcium ion-dependent exocytosis negative regulation of calcium ion-dependent exocytosis regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly regulation of integrin activation protein-containing complex assembly integrin activation positive regulation of integrin activation regulation of cell junction assembly cell junction assembly developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	membrane cellular anatomical entity cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle membrane cellular anatomical entity cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm organelle membrane secretory granule membrane cytosol cell periphery plasma membrane synapse glutamatergic synapse lipid droplet intracellular non-membrane-bounded organelle non-membrane-bounded organelle
C	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 cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic 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 cellular metabolic process biological regulation 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 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 positive regulation of cellular biosynthetic 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 regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of transferase activity negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process negative regulation of Rho-dependent protein serine/threonine kinase activity regulation of Rho-dependent protein serine/threonine kinase activity regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of protein serine/threonine kinase activity negative regulation of cellular process protein metabolic process negative regulation of macromolecule metabolic process negative regulation of molecular function regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation 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 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 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 protein localization localization cellular localization cellular macromolecule localization macromolecule 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 cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR041791	Krev interaction trapped protein 1, FERM domain C-lobe	Domain
A	IPR000299	FERM domain	Domain
A	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A	IPR043058	KRIT, N-terminal NPxY motif-rich domain superfamily	Homologous Superfamily
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR019748	FERM central domain	Domain
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR002110	Ankyrin repeat	Repeat
A	IPR019749	Band 4.1 domain	Domain
A	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A	IPR032022	KRIT, N-terminal NPxY motif-rich region	Domain
A	IPR051594	KRIT1/FRMD8	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR005225	Small GTP-binding domain	Domain
B	IPR020849	Small GTPase, Ras-type	Family
B	IPR001806	Small GTPase	Family
B	IPR038851	Ras-related protein Rap1	Family
C	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C	IPR000742	EGF-like domain	Domain
C	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
C	IPR001881	EGF-like calcium-binding domain	Domain
C	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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
B	Pharos: P61224	Kabuki syndrome lung adenocarcinoma
C	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