3TW8 | pdb_00003tw8

GEF domain of DENND 1B in complex with Rab GTPase Rab35

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3tw8b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3tw8d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	NTD-DENN	8049905	4006687	SCOP2 (2022-06-29)
C	SCOP2 Family	CTD-DENN	8051522	4007417	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	NTD-DENN	8055793	3002314	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Folliculin C-terminal domain-like	8051523	3002313	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Folliculin C-terminal domain-like	8051523	3002313	SCOP2B (2022-06-29)
B	SCOP2 Family	Ras-like monodomain GTPases	8056344	4004043	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ras-like P-loop GTPases	8056345	3002022	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8056345	3002022	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	Ras	e3tw8C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ras	ECOD (develop294)
A	Flavi_glycoprot	e3tw8A1	A: alpha bundles	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	H: SH3	T: SH3	F: Flavi_glycoprot	ECOD (develop294)
A	ATP_bind_3	e3tw8A2	A: alpha bundles	X: Metallothionein	H: HUP domains	T: HUP domains	F: ATP_bind_3	ECOD (develop294)
B		e3tw8B1	A: alpha bundles	X: Baculovirus p35 protein-related	H: Bet v1-like	T: Bet v1-like	F:	ECOD (develop294)
D	Ras	e3tw8D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Ras	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.450.200	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Longin module	CATH (4.3.0)
C	3.40.50.11500	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	DENN domain, C-terminal lobe	CATH (4.3.0)
C	6.10.140.1000	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	3.30.450.200	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Longin module	CATH (4.3.0)
A	3.40.50.11500	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	DENN domain, C-terminal lobe	CATH (4.3.0)
A	6.10.140.1000	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02141	DENN (AEX-3) domain (DENN)	DENN (AEX-3) domain	-	Family
A, C	PF03455	dDENN domain (dDENN)	dDENN domain	This region is always found associated with Pfam:PF02141. It is predicted to form a globular domain [1]. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family [1]. This N ...	This region is always found associated with Pfam:PF02141. It is predicted to form a globular domain [1]. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family [1]. This N-terminal region of DENN folds into a longin module, consisting of a central antiparallel beta-sheet layered between helix H1 and helices H2 and H3 (strands S1-S5). Rab35 interacts with dDENN via residues in helix 1 and in the loop S3-S4 [2].	Domain
A, C	PF03456	uDENN domain (uDENN)	uDENN domain	This region is always found associated with Pfam:PF02141. It is predicted to form an all beta domain [1].	Domain
B, 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, motili ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	DENN domain-containing protein 1B	small GTPase binding protein binding binding enzyme binding GTPase binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T-helper 2 cell cytokine production T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process type 2 immune response positive regulation of immune response regulation of T-helper 2 cell cytokine production adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T-helper 2 cell cytokine production T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process type 2 immune response positive regulation of immune response regulation of T-helper 2 cell cytokine production regulation of type 2 immune response cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of biological process regulation of cytokine production involved in immune response positive regulation of T-helper 2 cell cytokine production immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus regulation of immune response positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response positive regulation of type 2 immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response localization import into cell transport endocytosis establishment of localization vesicle-mediated transport establishment of protein localization protein transport macromolecule localization intracellular protein localization cellular localization intracellular transport localization within membrane endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane establishment of localization in cell	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen intracellular vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle cytoplasm vesicle cytosol
B, D	Ras-related protein Rab-35	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding GDP 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 cation binding metal ion binding	mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process localization transport plasma membrane to endosome transport establishment of localization vesicle-mediated transport mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process localization transport plasma membrane to endosome transport establishment of localization vesicle-mediated transport protein localization to endosome protein localization to organelle macromolecule localization intracellular protein localization establishment of protein localization protein transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor cellular localization establishment of localization in cell intracellular transport endosomal transport antigen processing and presentation immune system process localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane developmental process multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development cellular component organization generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development cellular component organization or biogenesis system development	cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle bounding membrane of organelle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane cell projection plasma membrane region cell projection membrane plasma membrane bounded cell projection intercellular bridge endosome membrane endosome recycling endosome recycling endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR005113	uDENN domain	Domain
A, C	IPR037516	Tripartite DENN domain	Domain
A, C	IPR005112	dDENN domain	Domain
A, C	IPR043153	DENN domain, C-terminal lobe	Homologous Superfamily
A, C	IPR040032	DENN domain-containing protein 1A/1B/1C	Family
A, C	IPR001194	cDENN domain	Domain
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR005225	Small GTP-binding domain	Domain
B, D	IPR001806	Small GTPase	Family
B, D	IPR041815	Rab35	Family
B, D	IPR050227	Ras-related protein Rab	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q6P3S1	primary biliary cholangitis Crohn disease asthma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Regional enteritis Sjogren syndrome endogenous depression ileocolitis large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma Pick disease primitive neuroectodermal tumor primary biliary cholangitis Crohn disease asthma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Regional enteritis Sjogren syndrome endogenous depression ileocolitis large cell medulloblastoma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma Pick disease primitive neuroectodermal tumor attention deficit hyperactivity disorder, inattentive type rheumatoid arthritis breast cancer tuberculosis Crohn's colitis cystic fibrosis endometriosis inflammatory bowel disease lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma psoriasis sarcoidosis breast carcinoma ductal breast carcinoma in situ hepatocellular carcinoma invasive ductal breast carcinoma
B, D	Pharos: Q15286	acute myeloid leukemia psoriasis Gaucher disease osteosarcoma

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.