4OIY | pdb_00004oiy

Crystal structure of Sec7p catalytic domain

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)
B	d4oiyb_	All alpha proteins	alpha-alpha superhelix	Sec7 domain	automated matches	automated matches	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4oiya1	All alpha proteins	alpha-alpha superhelix	Sec7 domain	automated matches	automated matches	yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d4oiya2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
B	SCOP2 Family	Sec7 domain-like	8080819	4001318	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Sec7 domain-like	8080820	3001279	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Sec7 domain-like	8080820	3001279	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	YajR_YAM	e4oiyB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (v294.1)
A	YajR_YAM	e4oiyA1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: YajR_YAM	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.220.20	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
B	1.10.1000.11	Mainly Alpha	Orthogonal Bundle	Arf Nucleotide-binding Site Opener	domain 2	CATH (4.3.0)
A	1.10.220.20	Mainly Alpha	Orthogonal Bundle	Annexin V	domain 1	CATH (4.3.0)
A	1.10.1000.11	Mainly Alpha	Orthogonal Bundle	Arf Nucleotide-binding Site Opener	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01369	Sec7 domain (Sec7)	Sec7 domain	The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the Pfam:PF00025 family [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein transport protein SEC7	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport cytoplasm protein quality control catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport cytoplasm protein quality control catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction biological regulation regulation of signal transduction ARF protein signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of ARF protein signal transduction intracellular signaling cassette regulation of cell communication signal transduction autophagosome assembly organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis process utilizing autophagic mechanism establishment of protein localization protein transport macromolecule localization intracellular protein localization cellular localization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport intercellular transport establishment of localization in cell	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm membrane intracellular vesicle membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle trans-Golgi network cytoplasm membrane intracellular vesicle COPI-coated vesicle COPI-coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle coated vesicle membrane vesicle membrane cytoplasmic vesicle Golgi-associated vesicle membrane coated vesicle Golgi-associated vesicle vesicle organelle membrane cytosol endosome late endosome transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR046455	Sec7/BIG1-like, C-terminal domain	Domain
A, B	IPR000904	Sec7 domain	Domain
A, B	IPR032691	Mon2/Sec7/BIG1-like, HUS domain	Domain
A, B	IPR023394	Sec7, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR032629	Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain	Domain
A, B	IPR015403	Mon2/Sec7/BIG1-like, HDS	Domain
A, B	IPR035999	Sec7 domain superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.