3CWZ

Structure of RAB6(GTP)-R6IP1 complex

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057420	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)
A	Ras	e3cwzA1	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)
B	PLAT	e3cwzB4	A: beta sandwiches	X: jelly-roll	H: Lipase/lipooxygenase domain (PLAT/LH2 domain) (From Topology)	T: Lipase/lipooxygenase domain (PLAT/LH2 domain)	F: PLAT	ECOD (1.6)
B	RUN	e3cwzB3	A: alpha arrays	X: RUN domain (From Topology)	H: RUN domain (From Topology)	T: RUN domain	F: RUN	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.20.58.900	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	6.10.250.800	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	2.60.60.20	Mainly Beta	Sandwich	Lipoxygenase-1	PLAT/LH2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF02759	RUN domain (RUN)	RUN domain	-	Family
B	PF01477	PLAT/LH2 domain (PLAT)	PLAT/LH2 domain	This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain bind ...	This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase Pfam:PF01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ras-related protein Rab-6A	protein binding binding protein domain specific 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 protein binding binding protein domain specific 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 cytoskeletal protein binding myosin V binding myosin 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	early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport protein methylation early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport protein methylation peptidyl-cysteine modification primary metabolic process macromolecule methylation peptidyl-cysteine methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process establishment of organelle localization organelle transport along microtubule minus-end-directed organelle transport along microtubule organelle localization microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process intra-Golgi vesicle-mediated transport protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum protein localization to Golgi apparatus protein localization to organelle localization within membrane protein localization to membrane protein localization to Golgi membrane antigen processing and presentation immune system process 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 endomembrane system membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endosome to plasma membrane transport vesicle intracellular organelle cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle cellular anatomical structure endomembrane system membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endosome to plasma membrane transport vesicle intracellular organelle cytoplasmic vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane secretory granule secretory granule membrane Golgi apparatus subcompartment Golgi apparatus trans-Golgi network Golgi membrane trans-Golgi network membrane acrosomal vesicle acrosomal membrane
B	Rab6-interacting protein 1	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process regulation of biological process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization biological regulation nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization	protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle intracellular organelle organelle protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle intracellular organelle organelle trans-Golgi network cytoplasm Golgi membrane bounding membrane of organelle organelle membrane cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding domain	Domain
A	IPR001806	Small GTPase	Family
A	IPR050227	Ras-related protein Rab	Family
B	IPR037213	RUN domain superfamily	Homologous Superfamily
B	IPR005113	uDENN domain	Domain
B	IPR004012	RUN domain	Domain
B	IPR037516	Tripartite DENN domain	Domain
B	IPR005112	dDENN domain	Domain
B	IPR047278	DENN domain-containing protein 5A/B	Family
B	IPR036392	PLAT/LH2 domain superfamily	Homologous Superfamily
B	IPR043153	DENN domain, C-terminal lobe	Homologous Superfamily
B	IPR047277	DENN domain-containing protein 5A/B, PLAT/LH2 domain	Domain
B	IPR001024	PLAT/LH2 domain	Domain
B	IPR001194	cDENN domain	Domain
B	IPR047295	DENN domain-containing protein 5A, second RUN domain	Domain
B	IPR047294	DENN domain-containing protein 5A, first RUN domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P20340	Alzheimer disease lung cancer Pick disease attention deficit hyperactivity disorder, inattentive type malignant glioma chronic obstructive pulmonary disease osteosarcoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM				PLAT domain

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.