8ENX

Crystal structure of beta'-COPI-WD40 domain Y33A mutant in complex with SARS-CoV-2 clientized spike tail heptapeptide.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
B	SCOP2B Superfamily	WD40 repeat-like	8057071	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8057071	3001694	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Coatomer subunit beta'	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 intracellular transport protein transport establishment of localization in cell 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 intracellular transport protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization intracellular protein transport endosomal transport late endosome to vacuole transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway vacuolar transport endosome transport via multivesicular body sorting pathway 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
C	Clientized spike tail heptapeptide	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity host cell surface binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity modulation by virus of host process virus-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism modulation by virus of host cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane regulation of biological process positive regulation of viral life cycle positive regulation of viral process biological regulation positive regulation of biological process modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm cellular anatomical structure membrane host extracellular space host cellular component cell periphery plasma membrane host intracellular membrane-bounded organelle host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endoplasmic reticulum-Golgi intermediate compartment membrane host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region host cell plasma membrane virion component virion membrane viral membrane viral envelope host cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR016453	Coatomer beta' subunit (COPB2)	Family
A, B	IPR006692	Coatomer, WD associated region	Domain
A, B	IPR050844	Coatomer complex subunit	Family
A, B	IPR001680	WD40 repeat	Repeat
A, B	IPR020472	G-protein beta WD-40 repeat	Repeat
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
C	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
C	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
C	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
C	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
C	IPR042578	Spike glycoprotein, betacoronavirus	Family
C	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
C	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
C	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
C	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
C	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
C	IPR002552	Spike glycoprotein S2, coronavirus	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.