8G78 | pdb_00008g78

Local refinement of SARS-CoV-2 spike/nanobody mixture complex around NTD

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092663	3002616	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092663	3002616	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain C-like	8092661	3002615	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8092469	3000120	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Coronavirus S1 glycoprotein, domain D-like	8092663	3002616	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)
E [auth F]	Integrin_A_Ig_3	e8g78F01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Integrin_A_Ig_3	ECOD (v294.1)
D [auth J]	Integrin_A_Ig_3	e8g78J01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Integrin_A_Ig_3	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth F], F [auth G], I [auth E]	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2026-04-17)
D [auth J], G [auth H], H [auth I]	Heavy Chain	IGHV1	-	spike glycoprotein	SAbDab (2026-04-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D]	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
A, B, C [auth D]	PF19209	Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)	Coronavirus spike glycoprotein S1, C-terminal	This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epide ...	This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth F], F [auth G], I [auth E]	Nanosota-6	-	-	-
D [auth J], G [auth H], H [auth I]	Nanosota-5	-	-	-
A, B, C [auth D]	Spike glycoprotein	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity 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 symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into 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 disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host tissue disruption of anatomical structure in another organism symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host fusion of virus membrane with host plasma membrane endocytosis involved in viral entry into host cell symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process symbiont-mediated-mediated suppression of host tetherin activity modulation of process of another organism 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 symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response entry receptor-mediated virion attachment to host cell	cellular anatomical structure membrane host cellular component host extracellular region other organism part 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 cellular anatomical structure membrane host cellular component host extracellular region other organism part 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, C [auth D]	IPR044873	Spike glycoprotein S2, coronavirus, heptad repeat 1	Domain
A, B, C [auth D]	IPR044366	Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2	Domain
A, B, C [auth D]	IPR018548	Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus	Domain
A, B, C [auth D]	IPR044341	Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like	Domain
A, B, C [auth D]	IPR032500	Spike glycoprotein S1, N-terminal domain, betacoronavirus-like	Domain
A, B, C [auth D]	IPR042578	Spike glycoprotein, betacoronavirus	Family
A, B, C [auth D]	IPR036326	Spike S1 subunit, receptor binding domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C [auth D]	IPR043002	Spike glycoprotein, N-terminal domain superfamily	Homologous Superfamily
A, B, C [auth D]	IPR044874	Spike glycoprotein S2, coronavirus, heptad repeat 2	Domain
A, B, C [auth D]	IPR043473	Spike glycoprotein S2 superfamily, coronavirus	Homologous Superfamily
A, B, C [auth D]	IPR043607	Coronavirus spike glycoprotein S1, C-terminal	Domain
A, B, C [auth D]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.