2W83

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4

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	d2w83b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2w83e_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2w83a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	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)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057436	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057436	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057436	3002022	SCOP2B (2022-06-29)
C	SCOP2 Family	JIP leucine zipper-like	8045644	4004588	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Leucine zipper-like	8091273	3001609	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Leucine zipper-like	8091273	3001609	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)
B	Ras	e2w83B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
E	Ras	e2w83E1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
A	Ras	e2w83A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.5.1000	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	arf6 gtpase in complex with a specific effector, jip4	CATH (4.3.0)
D	1.20.5.1000	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	arf6 gtpase in complex with a specific effector, jip4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain
C, D	PF16471	JNK-interacting protein leucine zipper II (JIP_LZII)	JNK-interacting protein leucine zipper II	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E	ADP-RIBOSYLATION FACTOR 6	thioesterase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity thioesterase binding protein binding binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding G protein activity molecular function regulator activity	protein localization regulation of localization cellular localization regulation of biological process regulation of cellular process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface regulation of cellular localization cellular macromolecule localization macromolecule localization negative regulation of cellular process protein localization regulation of localization cellular localization regulation of biological process regulation of cellular process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface regulation of cellular localization cellular macromolecule localization macromolecule localization negative regulation of cellular process regulation of protein localization to cell surface cellular process negative regulation of protein localization cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction cell division positive regulation of protein localization to plasma membrane positive regulation of biological process regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane localization within membrane regulation of protein localization to cell periphery protein localization to membrane positive regulation of protein localization regulation of protein localization to plasma membrane establishment of cell polarity establishment of epithelial cell polarity establishment or maintenance of cell polarity regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of developmental process nervous system development negative regulation of neuron projection development negative regulation of dendrite development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization 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 protein localization to cell division site protein localization to cleavage furrow positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization import into cell transport negative regulation of transport negative regulation of endocytosis vesicle-mediated transport regulation of endocytosis negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis regulation of dendritic spine development dendritic spine development organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cytoskeleton organization positive regulation of locomotion regulation of cell motility regulation of keratinocyte migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion positive regulation of keratinocyte migration keratinocyte migration cell adhesion cellular component disassembly regulation of focal adhesion disassembly focal adhesion disassembly cell junction disassembly cell-substrate junction disassembly positive regulation of cell-substrate junction organization cell junction organization positive regulation of focal adhesion disassembly cell-substrate junction organization regulation of cell-substrate junction organization hepaticobiliary system development gland development animal organ development liver development maintenance of synapse structure postsynapse organization cellular component maintenance maintenance of postsynaptic density structure cell junction maintenance maintenance of postsynaptic specialization structure postsynaptic density organization synapse organization postsynaptic specialization organization synaptic vesicle endocytosis synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell protein localization to endosome protein localization to organelle regulation of presynapse assembly cellular component biogenesis regulation of presynapse organization cellular component assembly cell junction assembly regulation of synapse structure or activity regulation of biological quality regulation of synapse assembly presynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization synapse assembly presynapse assembly positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis mitotic cytokinetic process mitotic cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cytokinetic process positive regulation of cell cycle mitotic cell cycle process cytokinetic process establishment of protein localization nitrogen compound transport intracellular transport protein transport intracellular protein transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport myeloid cell apoptotic process erythrocyte apoptotic process apoptotic process cell death programmed cell death ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cell projection assembly hepatocyte apoptotic process epithelial cell apoptotic process positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization actin filament organization regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization regulation of anatomical structure size filopodium assembly regulation of cell projection assembly regulation of filopodium assembly regulation of plasma membrane bounded cell projection assembly endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle synapse cell junction glutamatergic synapse Golgi apparatus endomembrane system ruffle cell projection cell leading edge plasma membrane bounded cell projection postsynapse midbody anchoring junction focal adhesion cell-substrate junction cell periphery cell cortex plasma membrane presynapse cell division site cleavage furrow plasma membrane region endosome membrane endosome recycling endosome cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane organelle membrane early endosome early endosome membrane Flemming body filopodium membrane actin-based cell projection filopodium cell projection membrane
C, D	C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4	JUN kinase binding protein binding binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding kinesin binding MAP-kinase scaffold activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity identical protein binding signaling receptor complex adaptor activity	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation localization organelle localization lysosome localization vacuolar localization regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell muscle structure development striated muscle cell differentiation muscle cell differentiation regulation of growth developmental growth cell projection organization neuron projection development regulation of cell morphogenesis cell projection morphogenesis negative regulation of growth negative regulation of dendrite extension neuron projection morphogenesis negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of developmental growth regulation of cellular component organization plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis cellular component organization cellular component organization or biogenesis dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth regulation of dendrite extension regulation of cell growth anatomical structure morphogenesis neuron development	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular organelle centrosome microtubule organizing center extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytoplasm cytosol vacuolar membrane membrane lytic vacuole vacuole intracellular membrane-bounded organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome perinuclear region of cytoplasm acrosomal vesicle intracellular vesicle endomembrane system cytoplasmic vesicle secretory granule secretory vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, E	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
A, B, E	IPR041838	ADP-ribosylation factor 6	Family
A, B, E	IPR005225	Small GTP-binding domain	Domain
A, B, E	IPR024156	Small GTPase superfamily, ARF type	Family
C, D	IPR034743	RH1 domain	Domain
C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C, D	IPR034744	RH2 domain	Domain
C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C, D	IPR039911	JNK-interacting protein 3/4	Family
C, D	IPR032486	JNK-interacting protein, leucine zipper II	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E	Pharos: P62330	astrocytic tumor juvenile dermatomyositis osteosarcoma psoriasis esophageal adenocarcinoma malignant pancreatic neoplasm ovarian cancer glioblastoma myopathy pancreatic intraductal papillary-mucinous neoplasm
C, D	Pharos: O60271	ulcerative colitis astrocytic tumor Down syndrome hereditary spastic paraplegia medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor Gaucher disease large cell medulloblastoma myopathy ovarian cancer Pick disease tuberculosis ulcerative colitis astrocytic tumor Down syndrome hereditary spastic paraplegia medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis atypical teratoid rhabdoid tumor Gaucher disease large cell medulloblastoma myopathy ovarian cancer Pick disease tuberculosis dermatomyositis glioblastoma malignant ependymoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor

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.