5CM9

Structural Basis for the Selectivity of Guanine Nucleotide Exchange Factors for the small G-protein Ral

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5cm9c_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
D	d5cm9d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8060862	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8060862	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras GEF	8018965	3000128	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ENTH/VHS domain-like	8018962	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ENTH/VHS domain-like	8018962	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras GEF	8018965	3000128	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)
C	PF00071	e5cm9C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
D	PF00071	e5cm9D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
A	PF00617,PF00618	e5cm9A1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: PF00617,PF00618	ECOD (1.6)
B	PF00617,PF00618	e5cm9B1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ras GEF (From Topology)	T: Ras GEF	F: PF00617,PF00618	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (4.3.0)
A	1.10.840.10	Mainly Alpha	Orthogonal Bundle	Son of Sevenless (SoS) protein	Chain S, domain 2	CATH (4.3.0)
B	1.20.870.10	Mainly Alpha	Up-down Bundle	Son of sevenless (SoS) protein	Chain S, domain 1	CATH (4.3.0)
B	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
C, D	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
A, B	PF00617	RasGEF domain (RasGEF)	RasGEF domain	-	Family
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Ras-related protein Ral-a	guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding PDZ domain binding protein domain specific 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 GTP binding purine ribonucleoside triphosphate binding	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus regulation of defense response regulation of response to biotic stimulus negative regulation of response to biotic stimulus regulation of response to external stimulus negative regulation of biological process regulation of response to stress innate immune response regulation of immune system process regulation of biological process negative regulation of response to stimulus immune response regulation of innate immune response negative regulation of immune response biological regulation defense response to symbiont regulation of response to stimulus negative regulation of immune system process immune system process negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response developmental process anatomical structure morphogenesis regulation of developmental process anatomical structure development cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis multicellular organismal process sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation epithelial cell differentiation gamete generation follicle cell of egg chamber development tissue migration cell differentiation ameboidal-type cell migration epithelial cell migration cell migration cell motility epithelium development oogenesis multicellular organismal reproductive process follicle cell of egg chamber migration tissue development epithelium migration epithelial cell development border follicle cell migration germ cell development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of ERBB signaling pathway regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling cell surface receptor signaling pathway ERBB signaling pathway regulation of cell communication positive regulation of signaling regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation R3/R4 cell fate commitment compound eye photoreceptor fate commitment sensory organ development photoreceptor cell differentiation establishment of ommatidial planar polarity visual system development establishment or maintenance of cell polarity eye morphogenesis multicellular organism development neurogenesis establishment of tissue polarity compound eye morphogenesis neuron differentiation morphogenesis of a polarized epithelium eye photoreceptor cell differentiation photoreceptor cell fate commitment animal organ morphogenesis sensory system development system development establishment of planar polarity eye photoreceptor cell fate commitment eye development neuron fate commitment animal organ development morphogenesis of an epithelium nervous system development R3/R4 cell differentiation generation of neurons tissue morphogenesis compound eye development sensory organ morphogenesis compound eye photoreceptor cell differentiation cell fate commitment negative regulation of signaling negative regulation of intracellular signal transduction intracellular signal transduction negative regulation of cell communication negative regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette negative regulation of cellular process regulation of JNK cascade regulation of MAPK cascade negative regulation of signal transduction MAPK cascade negative regulation of MAPK cascade small GTPase-mediated signal transduction Ras protein signal transduction	cell periphery plasma membrane membrane cellular anatomical entity Flemming body midbody cell division site cleavage furrow plasma membrane region
A, B	Ral guanine nucleotide dissociation stimulator-like 2	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	regulation of biological process regulation of cellular process negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process regulation of biological process regulation of cellular process negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of cellular process negative regulation of striated muscle cell apoptotic process cellular process apoptotic process programmed cell death cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette signal transduction positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling regulation of small GTPase mediated signal transduction regulation of Ral protein signal transduction Ral protein signal transduction	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR020849	Small GTPase, Ras-type	Family
C, D	IPR001806	Small GTPase	Family
C, D	IPR005225	Small GTP-binding protein domain	Domain
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR000159	Ras-associating domain	Domain
A, B	IPR008937	Ras-like guanine nucleotide exchange factor	Family
A, B	IPR019804	Ras guanine-nucleotide exchange factor, conserved site	Conserved Site
A, B	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A, B	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A, B	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A, B	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.