8DGW

Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	PF07654	e8dgwH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e8dgwH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth A]	PF07654	e8dgwA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth A]	PF07686	e8dgwA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth C]	PF07654	e8dgwC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth C]	PF07686	e8dgwC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth E]	PF07654	e8dgwE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth E]	PF07686	e8dgwE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth F]	PF07654	e8dgwF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth F]	PF07686	e8dgwF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth L]	PF07654	e8dgwL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth L]	PF07686	e8dgwL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth B]	PF07654	e8dgwB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth B]	PF07686	e8dgwB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth D]	PF07654	e8dgwD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F [auth D]	PF07686	e8dgwD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C [auth A], E [auth C], G [auth E]	Heavy Chain	IGHV1	-	spike protein s2'	SAbDab (2024-05-03)
B [auth L], D [auth B], F [auth D], H [auth F]	Light Chain	IGLV1	Lambda	spike protein s2'	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth G], J [auth I], K [auth J], L [auth K]	PF01601	Coronavirus spike glycoprotein S2 (CoV_S2)	Coronavirus spike glycoprotein S2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth A], E [auth C], G [auth E]	Antibody CC95.108 Fab heavy chain	-	-	-
B [auth L], D [auth B], F [auth D], H [auth F]	Antibody CC95.108 Fab light chain	-	-	-
I [auth G], J [auth I], K [auth J], L [auth K]	Spike protein S2'	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell endocytosis transport of virus	membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component 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 membrane cellular anatomical entity virion component virion membrane host intracellular membrane-bounded organelle host cellular component 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 viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth G], J [auth I], K [auth J], L [auth K]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR042578	Spike glycoprotein, betacoronavirus	Family
I [auth G], J [auth I], K [auth J], L [auth K]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
I [auth G], J [auth I], K [auth J], L [auth K]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
I [auth G], J [auth I], K [auth J], L [auth K]	IPR044339	Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR043614	Spike glycoprotein S2, coronavirus, C-terminal	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
I [auth G], J [auth I], K [auth J], L [auth K]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
I [auth G], J [auth I], K [auth J], L [auth K]	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 R01GM133198.