9AYR | pdb_00009ayr

Structure of a Ric1-Rgp1-Rab6 activation intermediate

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	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	PF08737	Rgp1 (Rgp1)	Rgp1	-	Family
A	PF07064	RIC1 C-terminal alpha solenoid region (RIC1)	RIC1 C-terminal alpha solenoid region	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	GTP-binding protein YPT6	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 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	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport cellular localization establishment of protein localization nitrogen compound transport intracellular transport protein transport establishment of localization in cell macromolecule localization localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport cellular localization establishment of protein localization nitrogen compound transport intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation retrograde transport, vesicle recycling within Golgi endosomal transport cytosolic transport retrograde transport, endosome to Golgi cellular response to heat response to heat response to abiotic stimulus response to temperature stimulus protein targeting establishment of protein localization to vacuole protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway establishment of protein localization to organelle protein localization to organelle vacuolar transport protein targeting to vacuole protein-containing complex localization Golgi to endosome transport post-Golgi vesicle-mediated transport autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly protein localization to phagophore assembly site cellular component organization or biogenesis	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane membrane cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane membrane phagophore assembly site
B	Guanine nucleotide exchange factor subunit RGP1	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular process cell division 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 anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system protein-containing complex Ric1-Rgp1 guanyl-nucleotide exchange factor complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system protein-containing complex Ric1-Rgp1 guanyl-nucleotide exchange factor complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex Golgi membrane membrane bounding membrane of organelle organelle membrane
A	Guanine nucleotide exchange factor subunit RIC1	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle endomembrane system protein-containing complex Ric1-Rgp1 guanyl-nucleotide exchange factor complex guanyl-nucleotide exchange factor complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle endomembrane system protein-containing complex Ric1-Rgp1 guanyl-nucleotide exchange factor complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex Golgi membrane membrane bounding membrane of organelle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR005225	Small GTP-binding domain	Domain
C	IPR001806	Small GTPase	Family
C	IPR050227	Ras-related protein Rab	Family
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR014848	Reduced growth phenotype protein 1	Family
A	IPR040096	RAB6A-GEF complex partner protein 1	Family
A	IPR009771	RIC1, C-terminal alpha solenoid region	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.