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192  structures 49  species 0  interactions 50  sequences 4  architectures

Family: bCoV_S1_N (PF16451)

Summary: Betacoronavirus-like spike glycoprotein S1, N-terminal

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Betacoronavirus-like spike glycoprotein S1, N-terminal Provide feedback

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].

Literature references

  1. Ou X, Guan H, Qin B, Mu Z, Wojdyla JA, Wang M, Dominguez SR, Qian Z, Cui S;, Nat Commun. 2017;8:15216.: Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1. PUBMED:28534504 EPMC:28534504

  2. Shang J, Wan Y, Liu C, Yount B, Gully K, Yang Y, Auerbach A, Peng G, Baric R, Li F;, PLoS Pathog. 2020;16:e1008392.: Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry. PUBMED:32150576 EPMC:32150576

  3. Qian Z, Ou X, Goes LG, Osborne C, Castano A, Holmes KV, Dominguez SR;, J Virol. 2015;89:8816-8827.: Identification of the Receptor-Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1. PUBMED:26085157 EPMC:26085157


This tab holds annotation information from the InterPro database.

InterPro entry IPR032500

The N-terminal domain of the coronavirus spike glycoprotein functions as a receptor binding domain. It binds carcinoembryonic antigen-related cell adhesion molecule 1 [PUBMED:21670291].

Domain organisation

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Alignments

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RP75
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(30)
Full
(50)
Representative proteomes UniProt
(1535)
NCBI
(1350)
Meta
(0)
RP15
(47)
RP35
(47)
RP55
(47)
RP75
(47)
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  Seed
(30)
Full
(50)
Representative proteomes UniProt
(1535)
NCBI
(1350)
Meta
(0)
RP15
(47)
RP35
(47)
RP55
(47)
RP75
(47)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: PDB:3r4d
Previous IDs: Spike_NTD;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R
Number in seed: 30
Number in full: 50
Average length of the domain: 297.80 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 23.22 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.7 26.4
Noise cut-off 21.4 21.0
Model length: 297
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the bCoV_S1_N domain has been found. There are 192 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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