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
Domain Annotation: ECOD 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)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein domain C-like	8092661	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S2 glycoprotein stalk-like	8092471	3000282	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)
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	Coronavirus spike S2 glycoprotein connector domain-like	8092473	3002562	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus receptor-binding domain-like	8092467	3001706	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)
A	F_UNCLASSIFIED	e8hc3A1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8hc3A3	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8hc3A2	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8hc3A4	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8hc3B4	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8hc3B2	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8hc3B3	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8hc3B1	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hc3C2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hc3C3	A: beta complex topology	X: Beta domain of coronavirus spike glycoprotein (From Topology)	H: Beta domain of coronavirus spike glycoprotein (From Topology)	T: Beta domain of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hc3C1	A: a+b three layers	X: Coronavirus spike protein receptor-binding domain (From Homology)	H: Coronavirus spike protein receptor-binding domain	T: Beta-coronavirus spike protein receptor-binding domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8hc3C4	A: a+b complex topology	X: S2 subunit of coronavirus spike glycoprotein (From Topology)	H: S2 subunit of coronavirus spike glycoprotein (From Topology)	T: S2 subunit of coronavirus spike glycoprotein	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth L]	F_UNCLASSIFIED	e8hc3L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth E]	F_UNCLASSIFIED	e8hc3E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth H]	F_UNCLASSIFIED	e8hc3H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth D]	F_UNCLASSIFIED	e8hc3D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)

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 (2023-09-15)
E [auth H], G [auth D]	Heavy Chain	IGHV3	-	spike glycoprotein	SAbDab (2023-09-15)

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Spike glycoprotein	host cell surface binding binding host cell surface receptor binding structural constituent of virion structural molecule activity identical protein binding 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 viral life cycle import into cell viral entry into host cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport 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 viral life cycle import into cell viral entry into host cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction movement in host localization entry into host endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus suppression by virus of host tetherin activity response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus mitigation of host antiviral defense response modulation by symbiont of host cellular process modulation by symbiont of host defense response response to biotic stimulus modulation by symbiont of host process response to host response to external biotic stimulus 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 cellular response to stimulus response to organic substance regulation of cellular process regulation of type I interferon-mediated signaling pathway negative regulation of biological process response to cytokine regulation of signal transduction perturbation of host innate immune response cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction regulation of biological process suppression of host innate immune response immune response regulation of innate immune response negative regulation of immune response suppression by virus of host type I interferon-mediated signaling pathway regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response perturbation of host immune response response to type I interferon suppression of host interferon-mediated signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling suppression of host defenses by symbiont perturbation by virus of host immune response negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress response to host immune response negative regulation of cellular process innate immune response cellular response to organic substance regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway biological regulation negative regulation of signal transduction cellular response to chemical stimulus mitigation of host defenses by symbiont negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway immune system process type I interferon-mediated signaling pathway suppression by virus of host innate immune response regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response suppression by symbiont of host immune response positive regulation of viral life cycle positive regulation of viral process 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	host extracellular space host cellular component cellular anatomical entity cell periphery plasma membrane 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 extracellular space host cellular component cellular anatomical entity cell periphery plasma membrane 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 cell host intracellular region host cell plasma membrane virion component virion membrane viral membrane viral envelope host cell surface
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.