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	8002782	4000272	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	cNMP-binding domain	8002783	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	8017527	3000084	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	cAMP-binding domain-like	8017525	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]	cNMP_binding_1	e2byvE3	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: cNMP_binding_1	ECOD (1.6)
A [auth E]	DEP	e2byvE4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DEP	ECOD (1.6)
A [auth E]	RasGEF_N	e2byvE2	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: RasGEF_N	ECOD (1.6)
A [auth E]	RasGEF	e2byvE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: RasGEF	ECOD (1.6)
A [auth E]	RA_2	e2byvE6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: RA_2	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]	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
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

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 adenyl ribonucleotide binding cyclic nucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding small GTPase binding protein binding binding enzyme binding GTPase binding protein-macromolecule adaptor activity molecular adaptor activity 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 cellular response to stimulus regulation of biological process regulation of cellular process regulated exocytosis transport secretion export from cell establishment of localization vesicle-mediated transport localization secretion by cell exocytosis cellular process calcium-ion regulated exocytosis cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of localization regulation of transport regulation of vesicle-mediated transport regulation of secretion regulation of secretion by cell regulation of exocytosis regulation of hormone levels cell-cell signaling hormone secretion signal release hormone transport regulation of biological quality protein localization positive regulation of cell communication establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization cellular macromolecule localization positive regulation of insulin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion positive regulation of protein localization cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion positive regulation of biological process positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport peptide secretion positive regulation of hormone secretion positive regulation of secretion amide transport positive regulation of cellular process positive regulation of peptide secretion regulation of signaling regulation of peptide transport regulation of establishment of protein localization regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization regulation of cell communication insulin secretion positive regulation of signaling regulation of synaptic vesicle cycle synaptic vesicle cycle vesicle-mediated transport in synapse establishment of localization in cell small GTPase-mediated signal transduction intracellular signal transduction intracellular signaling cassette	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 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]	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A [auth E]	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A [auth E]	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
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]	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 R01GM157729.