3BGF

X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab


ChainDomainClassArchitectureTopologyHomology
A3.30.70.1840 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Spike protein, C-terminal core receptor binding subdomain
A3.30.70.1840 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Spike protein, C-terminal core receptor binding subdomain
B3.30.70.1840 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Spike protein, C-terminal core receptor binding subdomain
B3.30.70.1840 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Spike protein, C-terminal core receptor binding subdomain
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
C2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
E2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
E2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
D2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
D2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
F2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins
F2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like Immunoglobulins

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
A, BPF01601Coronavirus spike glycoprotein S2 (CoV_S2)Coronavirus spike glycoprotein S2- Family
A, BPF16451Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)Betacoronavirus-like spike glycoprotein S1, N-terminalThis 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, BPF09408Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)Betacoronavirus spike glycoprotein S1, receptor bindingThis 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 ...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 translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion [1]. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilise both the S1 NTD and S1 RBD for viral entry [2]. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor [3,4].
Domain
C, EPF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
C, EPF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
D, FPF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, SSpike protein S1
C, LF26G19 Fab
B, HF26G19 Fab