3MKQ | pdb_00003mkq

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)
F	SCOP2B Superfamily	TPR-like	8048958	3001345	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TPR-like	8048958	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)
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)
C	SCOP2 Family	Coatomer WD associated region-like	8045227	4004362	SCOP2 (2022-06-29)
C	SCOP2 Family	WD40-repeat	8057074	4002744	SCOP2 (2022-06-29)
C	SCOP2 Family	WD40-repeat	8057075	4002744	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	TPR-like	8057073	3001345	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	WD40 repeat-like	8057077	3001694	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	WD40 repeat-like	8057076	3001694	SCOP2 (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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	VHP	e3mkqF1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Notch heterodimerization domain	T: Notch heterodimerization domain	F: VHP	ECOD (v294.1)
D	TPR_COPA_B	e3mkqD1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: TPR_COPA_B	ECOD (v294.1)
B	VHP	e3mkqB1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Notch heterodimerization domain	T: Notch heterodimerization domain	F: VHP	ECOD (v294.1)
E	PBP	e3mkqE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
E	TPR_COPA_B	e3mkqE3	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: TPR_COPA_B	ECOD (v294.1)
C	PBP	e3mkqC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
C	TPR_COPA_B	e3mkqC3	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: TPR_COPA_B	ECOD (v294.1)
A	WD40	e3mkqA1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: WD40	ECOD (v294.1)
A	Coatomer_WDAD	e3mkqA2	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Coatomer_WDAD	ECOD (v294.1)
A	TPR_COPA_B	e3mkqA3	A: a/b three-layered sandwiches	X: beta-clip	H: SET domain-like	T: SET domain-like	F: TPR_COPA_B	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
B	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF23953	COPA/B TPR domain (TPR_COPA_B)	COPA/B TPR domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 cellular localization establishment of protein localization intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein 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 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 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 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
A, C, E	Coatomer beta'-subunit	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 intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein 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 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 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR050844	Coatomer complex subunit	Family
B, D, F	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B, D, F	IPR010714	Coatomer, alpha subunit, C-terminal	Domain
B, D, F	IPR001680	WD40 repeat	Repeat
B, D, F	IPR006692	COPA/B, second beta-propeller domain	Domain
B, D, F	IPR047312	Coatomer subunit alpha, WD Associated Region	Domain
B, D, F	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, D, F	IPR056176	COPA/B, TPR domain	Domain
A, C, E	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, C, E	IPR016453	Coatomer beta' subunit (COPB2)	Family
A, C, E	IPR050844	Coatomer complex subunit	Family
A, C, E	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A, C, E	IPR001680	WD40 repeat	Repeat
A, C, E	IPR006692	COPA/B, second beta-propeller domain	Domain
A, C, E	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C, E	IPR056176	COPA/B, TPR domain	Domain