3KSY | pdb_00003ksy

Crystal structure of the Histone domain, DH-PH unit, and catalytic unit of the Ras activator Son of Sevenless (SOS)

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)
A	SCOP2 Family	Ras GEF	8018950	4001268	SCOP2 (2022-06-29)
A	SCOP2 Family	Pleckstrin-homology domain (PH domain)	8018970	4002395	SCOP2 (2022-06-29)
A	SCOP2 Family	Histone domain of Son of Sevenless (Sos-1)	8018971	4004029	SCOP2 (2022-06-29)
A	SCOP2 Family	DBL homology domain (DH-domain)	8018981	4001108	SCOP2 (2022-06-29)
A	SCOP2 Family	REM (Ras exchange motif)-like	8018982	4000381	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras GEF	8057967	3000128	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PH domain-like	8057964	3000134	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Core histone-like	8057963	3001387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DBL homology domain (DH-domain)	8057962	3000793	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ENTH/VHS domain-like	8057961	3000164	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Core histone-like	8057990	3001387	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	AP_endonuc_2	e3ksyA1	A: a/b three-layered sandwiches	X: Cytochrome P450	H: Cytochrome P450	T: Cytochrome P450	F: AP_endonuc_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A	1.20.900.10	Mainly Alpha	Up-down Bundle	Dbl Homology Domain	Chain A	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)
A	6.10.250.3060	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22697	SOS1/NGEF-like PH domain (SOS1_NGEF_PH)	SOS1/NGEF-like PH domain	This is a PH domain found in a diverse group of animal proteins such as Ephexin-1, SOS1 from human and related RhoGEFs [1-5].	Domain
A	PF00617	RasGEF domain (RasGEF)	RasGEF domain	-	Family
A	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	PF00621	RhoGEF domain (RhoGEF)	RhoGEF domain	Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that Pfam:PF00169 domains invariably occur C-terminal to RhoGEF/DH domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Son of sevenless homolog 1	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity SH3 domain binding protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity molecular condensate scaffold activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity SH3 domain binding protein binding binding protein domain specific binding protein heterodimerization activity protein dimerization activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity kinase binding enzyme binding protein kinase binding guanyl-nucleotide exchange factor activity epidermal growth factor receptor binding signaling receptor binding growth factor receptor binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus signal transduction multicellular organismal process regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation T cell activation lymphocyte proliferation regulation of immune system process regulation of multicellular organismal process T cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation cell activation regulation of T cell activation regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation response to stress response to ischemia cellular component organization sexual reproduction reproductive process multicellular organismal reproductive process cytoplasm organization cellular component organization or biogenesis female gamete generation vitellogenesis gamete generation B cell homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction 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 positive regulation of cellular process positive regulation of epidermal growth factor receptor signaling pathway regulation of ERBB signaling pathway regulation of signaling regulation of response to stimulus ERBB signaling pathway regulation of cell communication positive regulation of signaling immune response-regulating cell surface receptor signaling pathway immune response Fc receptor signaling pathway immune response-regulating signaling pathway Fc-epsilon receptor signaling pathway regulation of immune response developmental process head development brain morphogenesis animal organ development brain development nervous system development midbrain morphogenesis multicellular organism development anatomical structure morphogenesis central nervous system development midbrain development anatomical structure development animal organ morphogenesis system development regulation of pro-B cell differentiation regulation of developmental process cellular developmental process hemopoiesis cell development regulation of cell differentiation regulation of lymphoid progenitor cell differentiation pro-B cell differentiation cell differentiation lymphoid progenitor cell differentiation regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation multicellular organism growth developmental growth growth pericardium morphogenesis heart development epithelium development embryonic morphogenesis morphogenesis of an epithelium embryo development tissue development morphogenesis of an epithelial sheet circulatory system development tissue morphogenesis pericardium development blood vessel morphogenesis tube development vasculature development tube morphogenesis blood vessel development cardiac atrium morphogenesis cardiac chamber morphogenesis heart morphogenesis cardiac atrium development cardiac chamber development small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette Rac protein signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction positive regulation of small GTPase mediated signal transduction immune response-activating signaling pathway positive regulation of immune response positive regulation of immune system process immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response heart trabecula morphogenesis trabecula morphogenesis peripheral nervous system development glial cell development neurogenesis Schwann cell development gliogenesis glial cell differentiation Schwann cell differentiation epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process Ras protein signal transduction response to fibroblast growth factor cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway response to hormone cellular response to hormone stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to insulin cellular response to insulin stimulus axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development leukocyte migration cell migration cell motility regulation of leukocyte differentiation regulation of T cell differentiation in thymus mononuclear cell differentiation lymphocyte differentiation regulation of cell development regulation of T cell differentiation T cell differentiation in thymus T cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of hemopoiesis leukocyte differentiation neurotrophin TRK receptor signaling pathway neurotrophin signaling pathway myelination axon ensheathment ensheathment of neurons RNA metabolic process regulation of primary metabolic 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process eyelid development in camera-type eye sensory organ development eye development visual system development camera-type eye development sensory system development roof of mouth development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse somatodendritic compartment cell body neuronal cell body cell periphery plasma membrane membrane protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse somatodendritic compartment cell body neuronal cell body cell periphery plasma membrane membrane protein-containing complex catalytic complex GTPase complex postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization organelle asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008937	Ras-like guanine nucleotide exchange factor	Family
A	IPR019804	Ras guanine-nucleotide exchange factor, conserved site	Conserved Site
A	IPR000219	Dbl homology domain	Domain
A	IPR036964	Ras guanine-nucleotide exchange factor, catalytic domain superfamily	Homologous Superfamily
A	IPR035899	Dbl homology (DH) domain superfamily	Homologous Superfamily
A	IPR023578	Ras guanine nucleotide exchange factor domain superfamily	Homologous Superfamily
A	IPR055251	SOS1/NGEF-like, PH domain	Domain
A	IPR001849	Pleckstrin homology domain	Domain
A	IPR000651	Ras-like guanine nucleotide exchange factor, N-terminal	Domain
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR001895	Ras guanine-nucleotide exchange factors catalytic domain	Domain
A	IPR009072	Histone-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q07889	Noonan syndrome Noonan syndrome 4 hereditary gingival fibromatosis fibromatosis, gingival, 1 pancreatic ductal adenocarcinoma Adenocarcinoma of Lung Costello syndrome hepatocellular carcinoma hypertrophic cardiomyopathy malignant pancreatic neoplasm osteosarcoma tuberculosis cardiofaciocutaneous syndrome intellectual disability medulloblastoma Noonan syndrome Noonan syndrome 4 hereditary gingival fibromatosis fibromatosis, gingival, 1 pancreatic ductal adenocarcinoma Adenocarcinoma of Lung Costello syndrome hepatocellular carcinoma hypertrophic cardiomyopathy malignant pancreatic neoplasm osteosarcoma tuberculosis cardiofaciocutaneous syndrome intellectual disability medulloblastoma Noonan syndrome with multiple lentigines ovarian cancer Charcot-Marie-Tooth disease hydrops fetalis lung adenocarcinoma osteogenesis imperfecta

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.