7Q0I

Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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)
E [auth D]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	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 [auth H]	C1-set_1	e7q0iH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A [auth H]	V-set_12	e7q0iH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C [auth A]	C1-set_1	e7q0iA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth A]	V-set_12	e7q0iA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B [auth L]	C1-set	e7q0iL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
B [auth L]	V-set_3	e7q0iL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth B]	C1-set	e7q0iB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D [auth B]	V-set_3	e7q0iB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E [auth D]	Spike_NTD	e7q0iD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)
F [auth C]	Spike_NTD	e7q0iC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Spike_NTD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth D]	2.60.120.960	Mainly Beta	Sandwich	Jelly Rolls	Spike glycoprotein, N-terminal domain	CATH (utative)
F [auth C]	2.60.120.960	Mainly Beta	Sandwich	Jelly Rolls	Spike glycoprotein, N-terminal domain	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C [auth A]	Heavy Chain	IGHV3	-	spike protein s1	SAbDab (2025-01-17)
B [auth L], D [auth B]	Light Chain	IGLV3	Lambda	spike protein s1	SAbDab (2025-01-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth D], F [auth C]	PF16451	Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)	Betacoronavirus-like spike glycoprotein S1, N-terminal	This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like doma ...	This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognises sugar receptors [2]. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions [2]. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1 [2]. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV) [3]. Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth A]	Beta-43 heavy chain	-	-	-
B [auth L], D [auth B]	Beta-43 Fab light chain	-	-	-
E [auth D], F [auth C]	Spike protein S1	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 symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host 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 symbiont-mediated perturbation of host defense response suppression by virus of host tetherin activity biological process involved in interspecies interaction between organisms modulation by virus of host process virus-mediated perturbation of host defense response biological process involved in interaction with host biological process involved in symbiotic interaction 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 viral life cycle adhesion of symbiont to host viral gene expression viral translation fusion of virus membrane with host plasma membrane 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 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
E [auth D], F [auth C]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
E [auth D], F [auth C]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
E [auth D], F [auth C]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
E [auth D], F [auth C]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
E [auth D], F [auth C]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
E [auth D], F [auth C]	IPR042578	Spike glycoprotein, betacoronavirus	Family
E [auth D], F [auth C]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
E [auth D], F [auth C]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
E [auth D], F [auth C]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
E [auth D], F [auth C]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
E [auth D], F [auth C]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
E [auth D], F [auth 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.