3TJZ | pdb_00003tjz

Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3tjzd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d3tjza_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8089854	3002022	SCOP2B (2022-06-29)
A	SCOP2 Family	Ras-like monodomain GTPases	8089853	4004043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8089854	3002022	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)
F	Clat_adaptor_s	e3tjzF1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
C	Clat_adaptor_s	e3tjzC1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Clat_adaptor_s	ECOD (1.6)
E	Adaptin_N	e3tjzE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
B	Adaptin_N	e3tjzB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Adaptin_N	ECOD (1.6)
D	Ras	e3tjzD1	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	e3tjzA1	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)
F	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.2.0)
C	3.30.450.60	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.2.0)
E	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.2.0)
B	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.2.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF01217	Clathrin adaptor complex small chain (Clat_adaptor_s)	Clathrin adaptor complex small chain		Domain
B, E	PF01602	Adaptin N terminal region (Adaptin_N)	Adaptin N terminal region	-	Repeat
A, D	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Coatomer subunit zeta-1	-	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 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system COPI-coated vesicle membrane coat intracellular organelle cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system COPI-coated vesicle membrane coat intracellular organelle cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated vesicle Golgi-associated vesicle vesicle COPI vesicle coat Golgi apparatus membrane coated membrane intracellular membrane-bounded organelle COPI-coated vesicle membrane coated vesicle membrane cytoplasmic vesicle membrane organelle Golgi-associated vesicle membrane cytoplasm organelle membrane Golgi membrane
B, E	Coatomer subunit gamma	structural molecule 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 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell endoplasmic reticulum to Golgi vesicle-mediated transport establishment of organelle localization organelle transport along microtubule organelle localization microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system COPI-coated vesicle membrane coat intracellular organelle cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle membrane protein complex endomembrane system COPI-coated vesicle membrane coat intracellular organelle cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated vesicle Golgi-associated vesicle vesicle COPI vesicle coat Golgi apparatus membrane coated membrane intracellular membrane-bounded organelle COPI-coated vesicle membrane coated vesicle membrane cytoplasmic vesicle membrane organelle Golgi-associated vesicle membrane cytoplasm organelle membrane Golgi membrane cytosol endoplasmic reticulum-Golgi intermediate compartment endoplasmic reticulum
A, D	ADP-ribosylation factor 1	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	positive regulation of organelle organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of developmental process positive regulation of biological process cellular component organization positive regulation of developmental process anatomical structure development regulation of mitochondrial fusion cellular component organization or biogenesis mitochondrial fusion positive regulation of cellular process regulation of anatomical structure morphogenesis positive regulation of organelle organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of developmental process positive regulation of biological process cellular component organization positive regulation of developmental process anatomical structure development regulation of mitochondrial fusion cellular component organization or biogenesis mitochondrial fusion positive regulation of cellular process regulation of anatomical structure morphogenesis positive regulation of mitochondrial fusion mitochondrion organization developmental process regulation of biological process biological regulation regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization regulation of mitochondrion organization cellular process 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 intracellular protein localization intracellular protein transport catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism Golgi to plasma membrane transport post-Golgi vesicle-mediated transport localization within membrane vesicle-mediated transport vesicle-mediated transport to the plasma membrane Golgi vesicle transport fatty acid metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process regulation of ketone metabolic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of fatty acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process regulation of metabolic process lipid metabolic process organelle fission mitochondrial fission regulation of mitochondrial fission positive regulation of mitochondrial fission protein localization to Golgi membrane protein localization to Golgi apparatus protein localization to organelle protein localization to membrane endoplasmic reticulum to Golgi vesicle-mediated transport regulation of Golgi organization Golgi organization endomembrane system organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol cell periphery plasma membrane membrane organelle membrane contact site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR000804	Clathrin adaptor complex, small chain	Conserved Site
C, F	IPR022775	AP complex, mu/sigma subunit	Domain
C, F	IPR039652	Coatomer subunit zeta	Family
C, F	IPR011012	Longin-like domain superfamily	Homologous Superfamily
B, E	IPR016024	Armadillo-type fold	Homologous Superfamily
B, E	IPR002553	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Domain
B, E	IPR013040	Coatomer, gamma subunit, appendage, Ig-like subdomain	Domain
B, E	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
B, E	IPR011989	Armadillo-like helical	Homologous Superfamily
B, E	IPR032154	Coatomer subunit gamma, C-terminal	Domain
B, E	IPR017106	Coatomer gamma subunit	Family
B, E	IPR037067	Coatomer, gamma subunit, appendage domain superfamily	Homologous Superfamily
B, E	IPR012295	TBP domain superfamily	Homologous Superfamily
B, E	IPR009028	Coatomer/calthrin adaptor appendage, C-terminal subdomain	Homologous Superfamily
A, D	IPR005225	Small GTP-binding domain	Domain
A, D	IPR045872	ADP-ribosylation factor 1-5	Family
A, D	IPR024156	Small GTPase superfamily, ARF type	Family
A, D	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
A, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.