2D4Q

Crystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pleckstrin-homology domain (PH domain)	8018887	4002395	SCOP2 (2021-05-27)
A	SCOP2 Family	CRAL/TRIO domain	8018888	4003560	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	PH domain-like	8057934	3000134	SCOP2 (2021-05-27)
A	SCOP2 Superfamily	CRAL/TRIO domain	8057933	3001058	SCOP2 (2021-05-27)
B	SCOP2B Superfamily	PH domain-like	8057934	3000134	SCOP2B (2021-05-27)
B	SCOP2B Superfamily	CRAL/TRIO domain	8057933	3001058	SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF21877	e2d4qA2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF21877	ECOD (1.6)
A	PF13716	e2d4qA1	A: a/b three-layered sandwiches	X: SpoIIaa-like (From Topology)	H: SpoIIaa-like (From Topology)	T: SpoIIaa-like	F: PF13716	ECOD (1.6)
B	PF21877	e2d4qB2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: PF21877	ECOD (1.6)
B	PF13716	e2d4qB1	A: a/b three-layered sandwiches	X: SpoIIaa-like (From Topology)	H: SpoIIaa-like (From Topology)	T: SpoIIaa-like	F: PF13716	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.525.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphatidylinositol Transfer Protein Sec14p	CRAL-TRIO lipid binding domain	CATH (4.2.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.2.0)
B	3.40.525.10	Alpha Beta	3-Layer(aba) Sandwich	Phosphatidylinositol Transfer Protein Sec14p	CRAL-TRIO lipid binding domain	CATH (4.2.0)
B	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13716	Divergent CRAL/TRIO domain (CRAL_TRIO_2)	Divergent CRAL/TRIO domain	This family includes divergent members of the CRAL-TRIO domain family. This family includes ECM25 that contains a divergent CRAL-TRIO domain identified by Gallego and colleagues [1].	Domain
A, B	PF21877	PH domain-like (PH_NF1)	PH domain-like	This entry represents the NF1 PH domain, a pleckstrin homology (PH)-like domain of potentially novel function discovered within the neurofibromin protein. Neurofibromin is a Ras-specific GTPase-activating protein (RasGAP) encoded by the NF1 gene, mut ...	This entry represents the NF1 PH domain, a pleckstrin homology (PH)-like domain of potentially novel function discovered within the neurofibromin protein. Neurofibromin is a Ras-specific GTPase-activating protein (RasGAP) encoded by the NF1 gene, mutations in which cause neurofibromatosis type 1 (NF1). The NF1 PH domain forms a bipartite module with the Sec14p homologous segment, which together exhibit phospholipid binding activity. The domain interface architecture suggests a model of how the NF1 PH domain may regulate binding of a ligand by the Sec14 module [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Neurofibromin	phosphatidylethanolamine binding binding phospholipid binding lipid binding cation binding ion binding phosphatidylcholine binding quaternary ammonium group binding small molecule binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity phosphatidylethanolamine binding binding phospholipid binding lipid binding cation binding ion binding phosphatidylcholine binding quaternary ammonium group binding small molecule binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator 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 heart development animal organ development cellular developmental process astrocyte differentiation forebrain development cell development glial cell development neurogenesis astrocyte development gliogenesis cell differentiation head development forebrain astrocyte development brain development nervous system development central nervous system development glial cell differentiation cellular process forebrain astrocyte differentiation positive regulation of cell communication regulation of cellular process modulation of chemical synaptic transmission signaling positive regulation of biological process cell communication long-term synaptic potentiation synaptic signaling regulation of biological quality positive regulation of cellular process regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of long-term synaptic potentiation regulation of cell communication positive regulation of signaling cellular response to stimulus small GTPase-mediated signal transduction response to stimulus 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 negative regulation of Rac protein signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction negative regulation of response to stimulus Rac protein signal transduction negative regulation of small GTPase mediated signal transduction negative regulation of signal transduction regulation of Rac protein signal transduction regulation of response to stimulus regulation of catalytic activity negative regulation of catalytic activity regulation of transferase activity regulation of MAP kinase 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 cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process regulation of MAPK cascade 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 metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of protein serine/threonine kinase activity protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process negative regulation of protein kinase activity negative regulation of phosphorus metabolic process MAPK cascade regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade peripheral nervous system axon ensheathment peripheral nervous system development myelination Schwann cell development axon ensheathment ensheathment of neurons myelination in peripheral nervous system Schwann cell differentiation cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization artery development artery morphogenesis negative regulation of cell population proliferation regulation of stem cell proliferation cell population proliferation negative regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration epithelium migration tissue migration regulation of locomotion ameboidal-type cell migration regulation of cell migration regulation of endothelial cell migration blood vessel endothelial cell migration cell migration epithelial cell migration cell motility regulation of epithelial cell migration locomotion fibroblast proliferation brain morphogenesis forebrain morphogenesis animal organ morphogenesis negative regulation of locomotion negative regulation of cell motility negative regulation of cell migration leukocyte proliferation mast cell proliferation regulation of leukocyte migration leukocyte migration negative regulation of leukocyte migration negative regulation of immune system process immune system process regulation of immune system process regulation of leukocyte proliferation negative regulation of leukocyte proliferation regulation of mast cell proliferation negative regulation of mast cell proliferation regulation of cellular component organization postsynapse organization regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of cell differentiation regulation of neurogenesis regulation of gliogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis negative regulation of nervous system development negative regulation of cell differentiation negative regulation of developmental process regulation of glial cell differentiation negative regulation of gliogenesis negative regulation of cell development negative regulation of oligodendrocyte differentiation negative regulation of glial cell differentiation oligodendrocyte differentiation negative regulation of multicellular organismal process regulation of oligodendrocyte differentiation glial cell migration Schwann cell migration endothelial cell proliferation epithelial cell proliferation regulation of astrocyte differentiation negative regulation of astrocyte differentiation spinal cord development cell adhesion cell-matrix adhesion regulation of cell-matrix adhesion regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion muscle cell migration vascular associated smooth muscle cell migration smooth muscle cell migration positive regulation of molecular function positive regulation of hydrolase activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity regulation of vascular associated smooth muscle cell migration negative regulation of vascular associated smooth muscle cell migration regulation of smooth muscle cell migration negative regulation of smooth muscle cell migration cellular localization nitrogen compound transport transport localization secretion by cell gamma-aminobutyric acid transport signal release establishment of localization in cell organic anion transport synaptic transmission, GABAergic gamma-aminobutyric acid secretion carboxylic acid transport neurotransmitter secretion secretion export from cell acid secretion neurotransmitter transport establishment of localization organic acid transport amino acid transport signal release from synapse gamma-aminobutyric acid secretion, neurotransmission negative regulation of glial cell proliferation negative regulation of Schwann cell proliferation regulation of glial cell proliferation Schwann cell proliferation regulation of Schwann cell proliferation glial cell proliferation Ras protein signal transduction homeostatic process leukocyte apoptotic process regulation of programmed cell death positive regulation of mast cell apoptotic process positive regulation of myeloid cell apoptotic process mast cell homeostasis myeloid cell homeostasis positive regulation of leukocyte apoptotic process positive regulation of immune system process regulation of leukocyte apoptotic process myeloid cell apoptotic process positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process mast cell apoptotic process multicellular organismal-level homeostasis leukocyte homeostasis regulation of mast cell apoptotic process homeostasis of number of cells apoptotic process programmed cell death regulation of myeloid cell apoptotic process epithelium development epidermis development molting cycle process hair cycle developmental maturation tissue development skin development anatomical structure maturation skin epidermis development hair follicle development molting cycle hair cycle process hair follicle maturation adrenal gland development endocrine system development gland development neuron apoptotic process wound healing response to wounding negative regulation of cell-matrix adhesion negative regulation of cell adhesion negative regulation of cell-substrate adhesion myeloid leukocyte migration regulation of localization negative regulation of transport negative regulation of neurotransmitter transport regulation of secretion by cell negative regulation of secretion negative regulation of secretion by cell negative regulation of neurotransmitter secretion regulation of transport regulation of neurotransmitter transport regulation of secretion regulation of neurotransmitter secretion myeloid leukocyte differentiation hemopoiesis myeloid cell differentiation osteoclast differentiation leukocyte differentiation negative regulation of blood vessel morphogenesis negative regulation of angiogenesis negative regulation of vasculature development positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation behavior system process learning learning or memory observational learning nervous system process cognition amygdala development limbic system development negative regulation of endothelial cell proliferation negative regulation of epithelial cell proliferation protein localization negative regulation of protein transport establishment of protein localization negative regulation of nucleocytoplasmic transport nucleocytoplasmic transport regulation of protein localization nuclear transport negative regulation of intracellular protein transport regulation of protein localization to nucleus negative regulation of protein import into nucleus import into nucleus regulation of protein import into nucleus cellular macromolecule localization protein import into nucleus regulation of intracellular transport negative regulation of protein localization negative regulation of intracellular transport regulation of establishment of protein localization negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport negative regulation of protein localization to nucleus establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport intracellular protein transport neuroblast proliferation generation of neurons neural precursor cell proliferation positive regulation of signal transduction signal transduction in absence of ligand positive regulation of extrinsic apoptotic signaling pathway in absence of ligand extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus extrinsic apoptotic signaling pathway in absence of ligand cell surface receptor signaling pathway positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of apoptotic signaling pathway regulation of biosynthetic process cellular biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process negative regulation of neural precursor cell proliferation regulation of neuroblast proliferation negative regulation of neuroblast proliferation regulation of neural precursor cell proliferation positive regulation of neuron apoptotic process regulation of neuron apoptotic process sympathetic nervous system development autonomic nervous system development regulation of leukocyte differentiation regulation of osteoclast differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of osteoclast differentiation negative regulation of myeloid leukocyte differentiation regulation of hemopoiesis positive regulation of adenylate cyclase activity positive regulation of cyclase activity regulation of lyase activity regulation of adenylate cyclase activity regulation of cyclase activity positive regulation of lyase activity organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption tissue remodeling bone remodeling anatomical structure homeostasis extrinsic apoptotic signaling pathway via death domain receptors collagen fibril organization supramolecular fiber organization muscle cell proliferation smooth muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of neuronal synaptic plasticity regulation of long-term neuronal synaptic plasticity pallium development cerebral cortex development telencephalon development negative regulation of glial cell migration negative regulation of Schwann cell migration regulation of glial cell migration regulation of Schwann cell migration ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade camera-type eye morphogenesis sensory organ development eye development visual system development eye morphogenesis sensory organ morphogenesis camera-type eye development sensory system development metanephros development kidney development renal system development regulation of fibroblast proliferation negative regulation of fibroblast proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels pigmentation hepaticobiliary system development liver development ossification osteoblast differentiation regulation of synaptic transmission, GABAergic phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of vascular associated smooth muscle cell proliferation positive regulation of vascular associated smooth muscle cell proliferation regulation of smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation muscle structure development skeletal muscle organ development skeletal muscle tissue development muscle tissue development muscle organ development regulation of Ras protein signal transduction negative regulation of Ras protein signal transduction response to light stimulus visual learning visual behavior associative learning response to radiation synaptic transmission, glutamatergic L-amino acid transport L-glutamate import glutamate secretion acidic amino acid transport glutamate secretion, neurotransmission dicarboxylic acid transport smooth muscle tissue development neural tube development chordate embryonic development embryo development embryo development ending in birth or egg hatching	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse axon presynapse nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001251	CRAL-TRIO lipid binding domain	Domain
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR039360	Ras GTPase-activating protein	Family
A, B	IPR036865	CRAL-TRIO lipid binding domain superfamily	Homologous Superfamily
A, B	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A, B	IPR023152	Ras GTPase-activating protein, conserved site	Conserved Site
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR001936	Ras GTPase-activating domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P21359	neurofibromatosis juvenile myelomonocytic leukemia astrocytic tumor neurofibromatosis-Noonan syndrome schwannoma neurofibromatosis, familial spinal fibrosarcoma Watson syndrome intellectual disability liposarcoma acute myeloid leukemia glioblastoma malignant glioma melanoma subependymal giant cell astrocytoma neurofibromatosis juvenile myelomonocytic leukemia astrocytic tumor neurofibromatosis-Noonan syndrome schwannoma neurofibromatosis, familial spinal fibrosarcoma Watson syndrome intellectual disability liposarcoma acute myeloid leukemia glioblastoma malignant glioma melanoma subependymal giant cell astrocytoma neurofibroma neurofibromatosis type 1 cancer learning disability papillary adenoma childhood cerebral astrocytoma lung cancer chromosome 17q11.2 deletion syndrome, 1.4Mb pilocytic astrocytoma cutaneous melanoma malignant peripheral nerve sheath tumor protoplasmic astrocytoma sarcoma mixed glioma giant cell glioblastoma juvenile pilocytic astrocytoma perineurioma phaeochromocytoma colorectal cancer pleomorphic liposarcoma adenoma spindle cell sarcoma follicular thyroid adenoma Pheochromocytoma microcystic adenoma fibrillary astrocytoma gemistocytic astrocytoma anaplastic astrocytoma osteoarthritis leukemia peripheral nervous system neoplasm malignant mesothelioma 17q11.2 microduplication syndrome epithelioid sarcoma spinal cord disease nerve sheath neoplasm breast cancer osteosarcoma cerebral astrocytoma childhood malignant schwannoma malignant ependymoma melanocytic nevus psoriasis diffuse astrocytoma extra-adrenal sympathetic paraganglioma adult malignant schwannoma astrocytoma (excluding glioblastoma) hematopoietic and lymphoid system neoplasm oligodendroglioma ovarian cancer cerebrovascular disorder lung adenocarcinoma cholangiocarcinoma congenital anemia Dedifferentiated liposarcoma endometrial carcinoma multiple endocrine neoplasia type 2A adrenal gland pheochromocytoma glioma autism hydrocephalus brain disease

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM				CRAL/TRIO domain

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 R01GM133198.