4DX8 | pdb_00004dx8

ICAP1 in complex with KRIT1 N-terminus

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)
H [auth K]	SCOP2 Family	KRIT1 domain-like	8046007	4004818	SCOP2 (2022-06-29)
H [auth K]	SCOP2 Superfamily	Nudix	8053898	3000098	SCOP2 (2022-06-29)
E [auth H]	SCOP2B Superfamily	Nudix	8053898	3000098	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	PH domain-like	8053897	3000134	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	PH domain-like	8053897	3000134	SCOP2B (2022-06-29)
B	SCOP2 Family	ICAP1 domain-like	8044956	4004223	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PH domain-like	8053897	3000134	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	PH domain-like	8053897	3000134	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)
H [auth K]	CobA_CobO_BtuR	e4dx8K1	A: alpha bundles	X: Alpha-beta plaits	H: Phage tail protein-like	T: Phage tail protein-like	F: CobA_CobO_BtuR	ECOD (develop294)
G [auth J]	RB_A	e4dx8J1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (develop294)
F [auth I]	RB_A	e4dx8I1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: RB_A	ECOD (develop294)
E [auth H]	RGS	e4dx8H1	A: alpha bundles	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: RGS	ECOD (develop294)
D [auth E]		e4dx8E2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
C [auth D]		e4dx8D2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
B		e4dx8B2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
A	Bcl-2	e4dx8A1	A: alpha bundles	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: Bcl-2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth K]	3.30.70.2240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	KRIT, N-terminal Nudix domain, NPxY motif-rich region	CATH (4.3.0)
G [auth J]	3.30.70.2240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	KRIT, N-terminal Nudix domain, NPxY motif-rich region	CATH (4.3.0)
F [auth I]	3.30.70.2240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	KRIT, N-terminal Nudix domain, NPxY motif-rich region	CATH (4.3.0)
E [auth H]	3.30.70.2240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	KRIT, N-terminal Nudix domain, NPxY motif-rich region	CATH (4.3.0)
D [auth E]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
C [auth D]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	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
E [auth H], F [auth I], G [auth J], H [auth K]	PF16705	NUDIX, or N-terminal NPxY motif-rich, region of KRIT (NUDIX_5)	NUDIX, or N-terminal NPxY motif-rich, region of KRIT	NUDIX_5 is found in higher eukaryotes at the N-terminus of KRIT1 or Krev interaction trapped proteins. NUDIX_5 carries three NPxY-like motifs, and it is found to bind the integrin cytoplasmic-associated protein 1 ICAP1. In the absence of KRIT1 ICAP1 ...	NUDIX_5 is found in higher eukaryotes at the N-terminus of KRIT1 or Krev interaction trapped proteins. NUDIX_5 carries three NPxY-like motifs, and it is found to bind the integrin cytoplasmic-associated protein 1 ICAP1. In the absence of KRIT1 ICAP1 binds via its C-terminal PH/PTB fold domain to the integrin beta-1 cytoplasmic tail. Binding of KRIT1 to ICAP1 via NUDIX_5 out-competes the binding of ICAP1 to integrin cytoplasmic tails such that ICAP1 is sequestered in the nucleus. Integrin activation is thus prevented [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth H], F [auth I], G [auth J], H [auth K]	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
A, B, C [auth D], D [auth E]	Integrin beta-1-binding protein 1	GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding kinase binding enzyme binding protein kinase binding	regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function muscle cell migration myoblast migration cell migration cellular process cell motility cellular component organization cellular component biogenesis regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function muscle cell migration myoblast migration cell migration cellular process cell motility cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly integrin activation cellular component organization or biogenesis regulation of cellular process regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process activation of protein kinase B activity positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of cellular process regulation of biological process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular 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 regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus positive regulation of cell division cell division regulation of cell division regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization cell adhesion cell junction assembly positive regulation of cell-substrate adhesion regulation of cell-substrate junction organization focal adhesion assembly positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly negative regulation of cell adhesion negative regulation of cell adhesion involved in substrate-bound cell migration substrate-dependent cell migration negative regulation of phosphate metabolic process negative regulation of catalytic activity negative regulation of kinase activity negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of protein kinase activity negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process negative regulation of phosphorylation negative regulation of locomotion multicellular organismal process regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration angiogenesis negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration multicellular organism development tube morphogenesis regulation of cell migration anatomical structure development regulation of endothelial cell migration blood vessel endothelial cell migration locomotion negative regulation of cell migration blood vessel development system development developmental process blood vessel morphogenesis tube development regulation of cell migration involved in sprouting angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis regulation of locomotion anatomical structure formation involved in morphogenesis negative regulation of cell motility negative regulation of cell migration involved in sprouting angiogenesis cell population proliferation blood vessel endothelial cell proliferation involved in sprouting angiogenesis endothelial cell proliferation epithelial cell proliferation regulation of hydrolase activity regulation of GTPase activity animal organ development biomineral tissue development tissue development cell surface receptor signaling pathway Notch signaling pathway receptor clustering regulation of fibroblast migration fibroblast migration negative regulation of fibroblast migration ameboidal-type cell migration positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cellular response to vascular endothelial growth factor stimulus regulation of localization establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane establishment of protein localization to membrane regulation of establishment of protein localization establishment of localization protein targeting to membrane regulation of cellular localization regulation of protein targeting positive regulation of protein targeting to membrane negative regulation of protein targeting to membrane negative regulation of establishment of protein localization cellular developmental process cell differentiation negative regulation of cell-substrate junction organization negative regulation of cell-matrix adhesion negative regulation of cell junction assembly negative regulation of cellular component organization negative regulation of focal adhesion assembly negative regulation of cell-substrate adhesion positive regulation of locomotion positive regulation of cell migration positive regulation of endothelial cell migration positive regulation of cell motility cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin integrin-mediated signaling pathway regulation of substrate adhesion-dependent cell spreading negative regulation of substrate adhesion-dependent cell spreading substrate adhesion-dependent cell spreading positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of cell population proliferation regulation of Notch signaling pathway positive regulation of Notch signaling pathway regulation of tube diameter system process regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality blood circulation regulation of anatomical structure size regulation of integrin-mediated signaling pathway positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cytoskeleton organization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization tube formation	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle ruffle perinuclear region of cytoplasm centrosome microtubule organizing center centriolar satellite microtubule cytoskeleton cell periphery plasma membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth H], F [auth I], G [auth J], H [auth K]	IPR041791	Krev interaction trapped protein 1, FERM domain C-lobe	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR000299	FERM domain	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
E [auth H], F [auth I], G [auth J], H [auth K]	IPR043058	KRIT, N-terminal NPxY motif-rich domain superfamily	Homologous Superfamily
E [auth H], F [auth I], G [auth J], H [auth K]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
E [auth H], F [auth I], G [auth J], H [auth K]	IPR019748	FERM central domain	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR056485	KRIT1, ARM-repeats domain	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR011993	PH-like domain superfamily	Homologous Superfamily
E [auth H], F [auth I], G [auth J], H [auth K]	IPR002110	Ankyrin repeat	Repeat
E [auth H], F [auth I], G [auth J], H [auth K]	IPR019749	Band 4.1 domain	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR035963	FERM superfamily, second domain	Homologous Superfamily
E [auth H], F [auth I], G [auth J], H [auth K]	IPR032022	KRIT, N-terminal NPxY motif-rich region	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR057096	KRIT1/FRMD8, FERM domain C-lobe	Domain
E [auth H], F [auth I], G [auth J], H [auth K]	IPR051594	KRIT1/FRMD8	Family
A, B, C [auth D], D [auth E]	IPR019517	Integrin binding protein, ICAP-1	Family
A, B, C [auth D], D [auth E]	IPR006020	PTB/PI domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth H], F [auth I], G [auth J], H [auth K]	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
A, B, C [auth D], D [auth E]	Pharos: O14713	Craniofacial Abnormalities astrocytic tumor ductal breast carcinoma in situ large cell medulloblastoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor cutaneous lupus erythematosus gastric carcinoma malignant ependymoma medulloblastoma Pick disease dermatomyositis invasive ductal breast carcinoma malignant glioma Craniofacial Abnormalities astrocytic tumor ductal breast carcinoma in situ large cell medulloblastoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor cutaneous lupus erythematosus gastric carcinoma malignant ependymoma medulloblastoma Pick disease dermatomyositis invasive ductal breast carcinoma malignant glioma ovarian cancer

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.