8HC3

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 2 YB9-258 Fabs (2 RBD up)

Present annotations:

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Gene Product Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L], F [auth E]	Light Chain	IGKV1	Kappa	spike glycoprotein	SAbDab (2023-03-01)
E [auth H], G [auth D]	Heavy Chain	IGHV3	-	spike glycoprotein	SAbDab (2023-03-01)

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Spike glycoprotein	binding host cell surface receptor binding host cell surface binding protein binding identical protein binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell cellular process cellular component organization fusion of virus membrane with host plasma membrane membrane organization membrane fusion cellular component organization or biogenesis viral life cycle regulation of biological process involved in symbiotic interaction movement in host biological process involved in symbiotic interaction entry into host biological process involved in interspecies interaction between organisms regulation of viral entry into host cell positive regulation of viral entry into host cell viral entry into host cell positive regulation of biological process positive regulation of viral process regulation of biological process regulation of viral process biological process involved in interaction with host modulation by symbiont of entry into host biological regulation positive regulation by symbiont of entry into host regulation of viral life cycle positive regulation of viral life cycle virion attachment to host cell adhesion of symbiont to host adhesion of symbiont to host cell receptor-mediated virion attachment to host cell response to external stimulus response to biotic stimulus modulation by virus of host process mitigation of host antiviral defense response modulation by virus of host cellular process modulation of process of another organism suppression by virus of host tetherin activity response to external biotic stimulus modulation by symbiont of host process modulation by symbiont of host cellular process response to stimulus response to other organism modulation by symbiont of host defense response response to defenses of other organism response to host defenses response to host	host cellular component host cell cytoplasm host cell part host cell membrane host intracellular part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host intracellular region host cell host cell endoplasmic reticulum-Golgi intermediate compartment host cell endoplasmic reticulum-Golgi intermediate compartment membrane cellular anatomical entity host cell plasma membrane membrane viral envelope viral membrane virion component virion membrane
D [auth L], F [auth E]	Light chain of YB9-258	none	none	none
E [auth H], G [auth D]	Heavy chain of YB9-258	none	none	none

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.