7LQW
Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex with SARS-CoV-2 S2P spike
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
C [auth B] | SCOP2B Superfamily | SARS coronavirus receptor-binding domain-like | 8092467 | 3001706 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Coronavirus S2 glycoprotein stalk-like | 8092471 | 3000282 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Coronavirus spike S2 glycoprotein connector domain-like | 8092473 | 3002562 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain C-like | 8092661 | 3002615 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Concanavalin A-like lectins/glucanases | 8092469 | 3000120 | SCOP2B (2022-06-29) |
C [auth B] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain D-like | 8092663 | 3002616 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain C-like | 8092661 | 3002615 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Concanavalin A-like lectins/glucanases | 8092469 | 3000120 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Coronavirus S2 glycoprotein stalk-like | 8092471 | 3000282 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | SARS coronavirus receptor-binding domain-like | 8092467 | 3001706 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain D-like | 8092663 | 3002616 | SCOP2B (2022-06-29) |
D [auth C] | SCOP2B Superfamily | Coronavirus spike S2 glycoprotein connector domain-like | 8092473 | 3002562 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain D-like | 8092663 | 3002616 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Concanavalin A-like lectins/glucanases | 8092469 | 3000120 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Coronavirus S1 glycoprotein, domain C-like | 8092661 | 3002615 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Coronavirus S2 glycoprotein stalk-like | 8092471 | 3000282 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | SARS coronavirus receptor-binding domain-like | 8092467 | 3001706 | SCOP2B (2022-06-29) |
E [auth A] | SCOP2B Superfamily | Coronavirus spike S2 glycoprotein connector domain-like | 8092473 | 3002562 | 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] | V-set_8 | e7lqwH1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_8 | ECOD (1.6) |
B [auth L] | V-set | e7lqwL1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (1.6) |
C [auth B] | Spike_NTD | e7lqwB3 | A: beta sandwiches | X: jelly-roll | H: Concanavalin A-like | T: Concanavalin A-like lectins/glucanases | F: Spike_NTD | ECOD (1.6) |
C [auth B] | Spike_rec_bind_1 | e7lqwB2 | 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: Spike_rec_bind_1 | ECOD (1.6) |
C [auth B] | Spike_rec_bind | e7lqwB4 | 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: Spike_rec_bind | ECOD (1.6) |
C [auth B] | Corona_S2 | e7lqwB1 | 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: Corona_S2 | ECOD (1.6) |
D [auth C] | Spike_NTD | e7lqwC3 | A: beta sandwiches | X: jelly-roll | H: Concanavalin A-like | T: Concanavalin A-like lectins/glucanases | F: Spike_NTD | ECOD (1.6) |
D [auth C] | Spike_rec_bind_1 | e7lqwC4 | 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: Spike_rec_bind_1 | ECOD (1.6) |
D [auth C] | Spike_rec_bind | e7lqwC1 | 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: Spike_rec_bind | ECOD (1.6) |
D [auth C] | Corona_S2 | e7lqwC2 | 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: Corona_S2 | ECOD (1.6) |
E [auth A] | Spike_NTD | e7lqwA3 | A: beta sandwiches | X: jelly-roll | H: Concanavalin A-like | T: Concanavalin A-like lectins/glucanases | F: Spike_NTD | ECOD (1.6) |
E [auth A] | Spike_rec_bind_1 | e7lqwA4 | 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: Spike_rec_bind_1 | ECOD (1.6) |
E [auth A] | Spike_rec_bind | e7lqwA2 | 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: Spike_rec_bind | ECOD (1.6) |
E [auth A] | Corona_S2 | e7lqwA1 | 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: Corona_S2 | ECOD (1.6) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth H] | Heavy Chain | IGHV1 | - | spike glycoprotein | SAbDab (2024-12-13) |
B [auth L] | Light Chain | IGKV3 | Kappa | spike glycoprotein | SAbDab (2024-12-13) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
C [auth B], D [auth C], E [auth A] | PF01601 | Coronavirus spike glycoprotein S2 (CoV_S2) | Coronavirus spike glycoprotein S2 | - | Family |
C [auth B], D [auth C], E [auth A] | 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 ... | Domain |
C [auth B], D [auth C], E [auth A] | PF09408 | Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD) | Betacoronavirus spike glycoprotein S1, receptor binding | This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ... | Domain |
C [auth B], D [auth C], E [auth A] | 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 ... | Domain |