3MKQ

Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI vesicular coat

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Coatomer WD associated region-like	8045227	4004362	SCOP2 (2022-06-29)
C	SCOP2 Family	WD40-repeat	8057075	4002744	SCOP2 (2022-06-29)
C	SCOP2 Family	WD40-repeat	8057074	4002744	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	TPR-like	8057073	3001345	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	WD40 repeat-like	8057076	3001694	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	WD40 repeat-like	8057077	3001694	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	TPR-like	8057073	3001345	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	WD40 repeat-like	8057077	3001694	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	WD40 repeat-like	8057076	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8057077	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8057076	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TPR-like	8057073	3001345	SCOP2B (2022-06-29)
B	SCOP2 Family	Coatomer WD associated region-like	8045226	4004362	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TPR-like	8048958	3001345	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	TPR-like	8048958	3001345	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TPR-like	8048958	3001345	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)
C	PF00400	e3mkqC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
C	PF04053	e3mkqC2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF04053	ECOD (1.6)
C	PF04053	e3mkqC3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)
E	PF00400	e3mkqE1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
E	PF04053	e3mkqE2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF04053	ECOD (1.6)
E	PF04053	e3mkqE3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)
A	PF00400	e3mkqA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
A	PF04053	e3mkqA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF04053	ECOD (1.6)
A	PF04053	e3mkqA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)
B	PF04053	e3mkqB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)
D	PF04053	e3mkqD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)
F	PF04053	e3mkqF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04053	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
E	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
F	1.25.40.470	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF04053	Coatomer WD associated region (Coatomer_WDAD)	Coatomer WD associated region	-	Repeat
A, C, E	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, D, F	PF04053	Coatomer WD associated region (Coatomer_WDAD)	Coatomer WD associated region	-	Repeat
B, D, F	PF06957	Coatomer (COPI) alpha subunit C-terminus (COPI_C)	Coatomer (COPI) alpha subunit C-terminus	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Coatomer beta'-subunit	structural molecule activity	localization transport cellular process establishment of localization vesicle-mediated transport protein localization cellular localization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport establishment of localization in cell cellular macromolecule localization localization transport cellular process establishment of localization vesicle-mediated transport protein localization cellular localization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization intracellular protein transport	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle COPI-coated vesicle intracellular organelle COPI-coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle coated vesicle membrane vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle COPI-coated vesicle intracellular organelle COPI-coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle coated vesicle membrane vesicle membrane cytoplasmic vesicle Golgi-associated vesicle membrane organelle coated vesicle cytoplasm Golgi-associated vesicle vesicle organelle membrane Golgi membrane Golgi apparatus endomembrane system membrane coat protein-containing complex membrane protein complex coated membrane
B, D, F	Coatomer subunit alpha	protein binding binding ubiquitin binding ubiquitin-like protein binding structural molecule activity	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport protein localization cellular localization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport protein localization cellular localization establishment of protein localization nitrogen compound transport organic substance transport intracellular transport protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization intracellular protein transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum intracellular mRNA localization RNA localization endoplasmic reticulum to Golgi vesicle-mediated transport	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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated 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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated vesicle Golgi-associated vesicle vesicle COPI vesicle coat Golgi apparatus membrane cellular anatomical entity 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR001680	WD40 repeat	Repeat
A, C, E	IPR020472	G-protein beta WD-40 repeat	Repeat
A, C, E	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, C, E	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C, E	IPR016453	Coatomer beta' subunit (COPB2)	Family
A, C, E	IPR006692	Coatomer, WD associated region	Domain
B, D, F	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D, F	IPR011044	Quinoprotein amine dehydrogenase, beta chain-like	Homologous Superfamily
B, D, F	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, D, F	IPR016391	Coatomer subunit alpha	Family
B, D, F	IPR006692	Coatomer, WD associated region	Domain
B, D, F	IPR010714	Coatomer, alpha subunit, C-terminal	Domain
B, D, F	IPR001680	WD40 repeat	Repeat
B, D, F	IPR047312	Coatomer subunit alpha, WD Associated Region	Domain
B, D, F	IPR020472	G-protein beta WD-40 repeat	Repeat
B, D, F	IPR015943	WD40/YVTN repeat-like-containing 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 R01GM133198.