Annotations: 2BYV

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth E]	SCOP2 Family	DEP domain	8002779	4000306	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	cNMP-binding domain	8002783	4000272	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	cNMP-binding domain	8002782	4000272	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	Ras GEF	8002786	4001268	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	Ras-binding domain RBD	8004410	4000380	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	REM (Ras exchange motif)-like	8004411	4000381	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	Winged helix DNA-binding domain	8002780	3000034	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	cAMP-binding domain-like	8017525	3000084	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	cAMP-binding domain-like	8017527	3000084	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	Ras GEF	8002787	3000128	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	Ubiquitin-like	8004412	3000157	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	ENTH/VHS domain-like	8004415	3000164	SCOP2 (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 [auth E]	PF00027	e2byvE3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PF00027	ECOD (1.6)
A [auth E]	PF00610	e2byvE4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF00610	ECOD (1.6)
A [auth E]	PF00617	e2byvE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: PF00617	ECOD (1.6)
A [auth E]	PF00618	e2byvE2	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: PF00618	ECOD (1.6)
A [auth E]	F_UNCLASSIFIED	e2byvE6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	2.60.120.10	Mainly Beta	Sandwich	Jelly Rolls	Jelly Rolls	CATH (4.3.0)
A [auth E]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A [auth E]	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (4.3.0)
A [auth E]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A [auth E]	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E]	PF00617	RasGEF domain (RasGEF)	RasGEF domain	-	Family
A [auth E]	PF00618	RasGEF N-terminal motif (RasGEF_N)	RasGEF N-terminal motif	A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.	Domain
A [auth E]	PF00610	Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) (DEP)	Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)	The DEP domain [1] is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) prot ...	The DEP domain [1] is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting [4-5]. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit [6-7].	Domain
A [auth E]	PF00027	Cyclic nucleotide-binding domain (cNMP_binding)	Cyclic nucleotide-binding domain	This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E]	RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4	small GTPase binding protein binding binding enzyme binding GTPase binding protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding small GTPase binding protein binding binding enzyme binding GTPase binding protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding cAMP binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis positive regulation of locomotion regulation of biological process regulation of cell motility regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration biological regulation positive regulation of biological process positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process trans-synaptic signaling regulation of signaling negative regulation of signaling signaling modulation of chemical synaptic transmission negative regulation of biological process cell-cell signaling negative regulation of synaptic transmission negative regulation of cell communication cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling negative regulation of cellular process regulation of cell communication regulation of hormone levels hormone secretion signal release hormone transport regulation of biological quality regulation of cellular component organization postsynapse organization regulation of postsynapse organization cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization cellular component organization or biogenesis protein localization establishment of protein localization cellular localization nitrogen compound transport protein localization to extracellular region peptide secretion amide transport cellular macromolecule localization organic substance transport establishment of protein localization to extracellular region protein secretion peptide transport protein transport peptide hormone secretion macromolecule localization insulin secretion regulation of localization regulation of transport regulation of synaptic vesicle cycle synaptic vesicle cycle regulation of vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell positive regulation of cell communication multicellular organismal process system process regulation of system process positive regulation of transmission of nerve impulse neuronal action potential regulation of transmission of nerve impulse positive regulation of nervous system process regulation of multicellular organismal process regulation of neuronal action potential regulation of action potential nervous system process action potential transmission of nerve impulse regulation of nervous system process positive regulation of action potential positive regulation of multicellular organismal process positive regulation of neuronal action potential regulation of membrane potential regulation of neuron projection development regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus response to stimulus adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of protein localization positive regulation of establishment of protein localization positive regulation of secretion by cell positive regulation of protein transport regulation of secretion by cell positive regulation of secretion regulation of establishment of protein localization regulation of protein transport positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport regulation of cellular localization positive regulation of protein localization protein localization to synapse regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to cell periphery protein localization to postsynaptic membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse regulation of exocytosis positive regulation of insulin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion regulation of hormone secretion regulation of peptide secretion positive regulation of hormone secretion positive regulation of peptide secretion regulation of peptide transport regulation of insulin secretion positive regulation of signaling	photoreceptor inner segment cellular anatomical entity axon synapse neuron projection axon terminus cone cell pedicle plasma membrane bounded cell projection presynapse cell projection distal axon cell junction neuron projection terminus intracellular anatomical structure photoreceptor inner segment cellular anatomical entity axon synapse neuron projection axon terminus cone cell pedicle plasma membrane bounded cell projection presynapse cell projection distal axon cell junction neuron projection terminus intracellular anatomical structure cytoplasm cytosol cell periphery basal part of cell membrane plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane cluster of actin-based cell projections brush border somatodendritic compartment dendrite dendritic tree glutamatergic synapse membrane-bounded organelle non-motile cilium 9+0 non-motile cilium cilium photoreceptor outer segment photoreceptor cell cilium organelle neuron spine dendritic spine postsynapse cell body neuronal cell body apical part of cell apical plasma membrane growth cone site of polarized growth protein-containing complex neuron to neuron synapse hippocampal mossy fiber to CA3 synapse excitatory synapse postsynaptic density postsynaptic specialization asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E]	IPR000591	DEP domain	Domain
A [auth E]	IPR008937	Ras-like guanine nucleotide exchange factor	Family
A [auth E]	IPR019804	Ras guanine-nucleotide exchange factor, conserved site	Conserved Site
A [auth E]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A [auth E]	IPR000595	Cyclic nucleotide-binding domain	Domain
A [auth E]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth E]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A [auth E]	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A [auth E]	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A [auth E]	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A [auth E]	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A [auth E]	IPR018490	Cyclic nucleotide-binding domain superfamily	Homologous Superfamily
A [auth E]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

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.