The ESC Beacon API enables the search query across the Esc (Immune escape variants in SARS-CoV-2). The idea behind creating the Beacon API is to make the genomic data discoverable for the research and clinical purpose in the public domain.
The ESC Beacon API allows the user to search queries related to the presence or absence of specific variants in a given dataset. The Beacon API has one endpoint: /beacon?Variant; query interface is provided by the beacon endpoint. The beacon API specification is written in OpenAPI. The ESC Beacon API v1.0.0 is a read-only API. It uses JSON in requests and responses and standard HTTPS for information transfer.
This document also describes the ESC Beacon API in detail and provides information on the specific endpoints, request formats, and response.
Version : 1.0.0
| Parameter (* mandatory, one of these is mandatory) | Description | Type | Example |
|---|---|---|---|
| Variant | Change in amino acids in standard format | string | N440K |
Content-type:application/json
Payload: Beacon Response object
| Properties | Description | Type | Example |
|---|---|---|---|
| beaconId | Identifier of the beacon, as defined in Beacon | string | |
| apiVersion | Version of the API. | string | 1.0.0 |
| exists | Indicator of whether the given query was observed in the dataset queried. This should be non-null, unless there was an error, in which case error has to be non-null. | string | TRUE |
| updatedDate | The time the dataset was updated in (ISO 8601 format). | string | "2021-07-20" |
| requestParameter | The request that is sent to the Beacon. | object | BeaconRequest Object |
| datasetResponses | The response that the user receives from the Beacon | object | BeaconDatasetResponse Object |
| error | The error message and the appropriate HTTP status code | object | null |
A GET request like this:
{
"beaconId": "esc-beacon",
"apiVersion": "1.0.0",
"exists": true,
"error": null,
"updatedDate": "2021-09-14",
"requestParameters": {
"variant": "N440K",
"includeDatasetResponses": "ALL"
},
"datasetResponses": {
"exists": true,
"data": [
{
"_id": {
"$oid": "613deea3d2b575ce3b35814b"
},
"Gene": "S",
"NCBI_Gene_ID": 43740568,
"Gene_ID_Link": "https:\/\/www.ncbi.nlm.nih.gov\/gene\/43740568",
"Gene_Location": "NC_045512.2:21563-25384",
"Gene_Location_link": "https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?hgtgroup_map_close=0&hgtgroup_genes_close=0&hgtgroup_uniprot_close=0&hgtgroup_immu_close=0&hgtgroup_rna_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0&hgsid=950344573_A9vhn3kpWNAevyURQKIFZD7Av59E&position=NC_045512.2%3A21563-25384&hgt.positionInput=NC_045512.2%3A21563-25384&goButton=go&db=wuhCor1&c=NC_045512v2&l=265&r=21555&pix=950&dinkL=2.0&dinkR=2.0",
"Variant_Position": 22882,
"Reference_Base": "T",
"Alternate_Base": "G",
"Variant": "22882T>G",
"Amino_Acid_Position": 440,
"Reference_Amino_Acid": "N (Asn)",
"Alternate_Amino_acid": "K (Lys)",
"AA_Change": "N440K",
"Type_of_Mutation": "Resistant to mAbs",
"VoCs_VoIs": "None",
"VoCs_VoIs_link": "None",
"VoCs_VoIs_Aliases": "None",
"VoCs_VoIs_Aliases_link": "None",
"VoCs_VoIs_Description": "None",
"PROTEIN_NAME": "Spike glycoprotein",
"UNIPROT_PROTEIN_ID": "P0DTC2",
"UNIPROT_PROTEIN_ID_LINK": "https:\/\/www.uniprot.org\/uniprot\/P0DTC2#family_and_domains",
"PROTEIN_LENGTH": "1273 amino acids",
"Protein_Description": "Spike protein is one of the structural proteins of SARS-CoV-2. The monomeric protein consists of one large ectodomain, a single-pass transmembrane anchor, and a short intracellular tail at C-terminus. It encompasses 22 glycosylation sites. S protein cleaves into two subunits namely S1 and S2 following receptor recognition. Receptor Binding Domain (RBD) in S1 subunit plays a major role in ACE2 receptor binding.",
"Protein_Domain": "Receptor Binding Domain (RBD) of SARS-CoV-2. The SARS-CoV-2 RBD has a twisted five-stranded antiparallel \u03b2 sheet (\u03b21, \u03b22, \u03b23, \u03b24 and \u03b27) with short connecting helices and loops that form the core. Between the \u03b24 and \u03b27 strands in the core, there is an extended insertion containing the short \u03b25 and \u03b26 strands, \u03b14 and \u03b15 helices and loops. ",
"Domain_position": "SARS-CoV-2 RBD (residues Arg319\u2013Phe541)",
"Function_of_the_Domain": "Receptor Binding Domain is a vital immunogenic fragment in the Spike protein of SARS-CoV-2 virus that binds to specific endogenous receptors in the host. SARS-CoV-2 gains entry and causes infection in humans by binding to ACE2 receptor.",
"Epitope_Type": "Linear peptide",
"IEDB_Reference_B_cell_epitope_Sequence": "KLPDDFTGCVIAWNSNNLDS (424-443)##LPDDFTGCVIAWNSNNLD (425-442)## VIAWNSNNLDSKVGGNYN (433-450)##IAWNSNNLDSKVGGNYNYLY (434-453)",
"B_cell_Epitope_ID": "1309501##1087618##1087772## 1309490",
"IEDB_Antigen_Accession": "QII57161.1##QHD43416.1##QII57161.1##QHD43416.1",
"IEDB_linkout": "",
"Predicted_B_cell_Epitopes": "LPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERD (425-467)##PDDFTGCVIAWNSNN (426-440)##DDFTGCVIAWNSNNL (427-441)##GCVIAWNSNNLDSKV (431-445)##WNSNNLDSKVGGNYN (436-450)##NLDSKVGGNY (440-449)",
"Predicted_B_cell_epitope_Binding_affinity": "1074979##1310707##1069293##1310437##1310945##1075002",
"Predicted_T_cell_Epitopes": "YP_009724390.1##QKE11719.1##QHD43416.1##QKE11719.1##QKE11719.1##YP_009724390.1",
"Predicted_T_cell_epitope_Binding_affinity": "",
"Antibody_Name": "C135",
"Antibody_Category_and_Description": "Isotype - Mouse IgG1 ; Anti-Human CD4. Class II antibody. hNAbs that overlap with the ACE2 binding site and recognize both \u201cup\u201d and \u201cdown\u201d RBD conformations",
"ABCD_(AntiBodies_Chemically_Defined)_Database_ID": "ABCD_AT512",
"Antibody_linkout_": "https:\/\/web.expasy.org\/abcd\/ABCD_AT512",
"Antibody_Details": "",
"Study_Type": "Experimental methods",
"Details_of_the_study": "Two plaque-purified variants designated rVSV\/SARS-CoV-2\/GFP1D7 and rVSV\/SARS-CoV-2\/GFP2E1 that encode F157S\/R685M (1D7) and D215G\/R683G (2E1) substitutions were used. For selection of viruses resistant to plasma or monoclonal antibodies, rVSV\/SARS-CoV-2\/GFP1D7 and rVSV\/SARS-CoV-2\/GFP2E1 populations containing 106 infectious particles were used. rVSV\/SARS-CoV-2\/GFP1D7 and rVSV\/SARS-CoV-2\/GFP2E1 were passaged generate diversity, incubated with dilutions of monoclonal antibodies (10 \u03bcg\/ml, 5 \u03bcg\/ml) or COVID19 plasma (1:50, 1:250, 1:500) for 1 hr at 37 \u00b0C. Then, the virus-antibody mixtures were incubated with 2 \u00d7 105 293T\/ACE2(B) cells in 12-well plates. Two days later, the cells were imaged and supernatant from the wells containing the highest concentration of plasma or monoclonal antibodies that showed evidence of viral replication (GFP-positive foci) or large numbers of GFP-positive cells was harvested. For the identification of putative antibody resistance mutations, RNA was isolated from aliquots of supernatant containing selected viral populations or individual plaque-purified variants using Trizol-LS. The purified RNA was subjected to reverse transcription using random hexamer primers and Superscript III reverse transcriptase (Thermo Fisher Scientific, US). The cDNA was amplified using Phusion (NEB, US) and primers flanking RBD encoding sequences. Alternatively, a fragment including the entire S-encoding sequence was amplified using primers targeting VSV-M and VSV-L. The PCR products were gel-purified and sequenced either using Sanger-sequencing or NGS, followed by systematic sequence analysis. ",
"RefGene_Function": "Protein Coding Region",
"Variation_Type": "Nonsynonymous SNV",
"SIFT_Score": 0.73,
"SIFT_Prediction": "Tolerated",
"GERP": -3.3,
"PhyloP": 0.135937,
"PhastCons": 0,
"Uniprot_Domains": "Disulf_bond",
"UNIPROT_Disulphite_Bond": "BetaCoV_S1-CTD",
"UNIPROT_glyphos": "NA",
"UNIPROT_Transmembrane": "NA",
"IEDB_B-Cell_Epitopes": "Surface glycoprotein_IAWNSNNLDSK",
"IEDB_CD4_Epitopes": "NA",
"IEDB_cd4Epitope_Score": "NA",
"IEDB_CD8_Epitopes": "NA",
"IEDB_cd8Epitope_Score": "NA",
"MPDI_Potential_Immunogenic_Regions": "NA",
"MPDI_Potential_Immunodominant_Epitopes": "NA",
"ARTIC_Primers": "nCoV-2019_75_RIGHT",
"RT-PCR_Primers\/Probes": "NA",
"Sequencing_Error_Sites": "NA",
"Homoplasic_Positions": "NA",
"Hypermutable_Sites": "NA",
"Global_Variant_Frequency": 0.00206889,
"Geographical_Variant_Frequency": "Africa(0.00600236)##Asia(0.0153999)##Europe(0.000959122)##NorthAmerica(0.00114642)##Oceania(0.000559884)##SouthAmerica(0.00306081)",
"Reference": "Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., Gaebler, C., Agudelo, M., Cho, A., Wang, Z., Gazumyan, A., Cipolla, M., Luchsinger, L., Hillyer, C. D., Caskey, M., \u2026 Bieniasz, P. D. (2020). Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. ELife, 9, 1. https:\/\/doi.org\/10.7554\/elife.61312",
"Reference_Link": "https:\/\/elifesciences.org\/articles\/61312",
"hc-key": "af,as,eu,na,oc,sa",
"value": "0.00600236,0.0153999,0.000959122,0.00114642,0.000559884,0.00306081",
"Experiment_type": "Mutations in isolation",
"Neutralization_quantification": "C135 reduced infection by ~ 100 fold",
"Ensembl_Gene_ID": "ENSSASG00005000004",
"Ensembl_Gene_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Gene\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"Ensembl_Transcript_ID": "ENSSAST00005000004.1",
"Ensembl_Transcript_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Transcript\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"CDS_Position": 1320,
"Codons": "aaT\/aaG",
"Ensembl_Variant_ID": "MN908947.3:22882:T:G",
"Variant_Location": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Location\/View?db=core;r=MN908947.3:22872-22892",
"HGVS_Nomenclature": "None",
"Variant_Population_genetics": "None",
"Variant_Sample_Genotype": "None",
"Antibody_Generation": "The human plasma samples COV-47, COV-72 and COV-107 and monoclonal antibodies C144, C135 and C121 used in this study were previously reported",
"SARS-CoV-2_Mutants_Generation": "The pSARS-CoV-2 protein expression plasmid containing a C-terminally truncated SARS-CoV-2 S protein (pSARS-CoV-2\u039419) containing desired muations was generated. 293T cells were transfected with pHIVNLGagPol, pCCNanoLuc2AEGFP and a WT or mutant SARS-CoV-2 expression plasmid (pSARS-CoV-2\u039419) using polyethyleneimine. ",
"Antibody_Binding_escape_Profile": "Flow cytometry or NanoLuc luciferase assays"
},
{
"_id": {
"$oid": "613deea3d2b575ce3b35814c"
},
"Gene": "S",
"NCBI_Gene_ID": 43740568,
"Gene_ID_Link": "https:\/\/www.ncbi.nlm.nih.gov\/gene\/43740568",
"Gene_Location": "NC_045512.2:21563-25384",
"Gene_Location_link": "https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?hgtgroup_map_close=0&hgtgroup_genes_close=0&hgtgroup_uniprot_close=0&hgtgroup_immu_close=0&hgtgroup_rna_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0&hgsid=950344573_A9vhn3kpWNAevyURQKIFZD7Av59E&position=NC_045512.2%3A21563-25384&hgt.positionInput=NC_045512.2%3A21563-25384&goButton=go&db=wuhCor1&c=NC_045512v2&l=265&r=21555&pix=950&dinkL=2.0&dinkR=2.0",
"Variant_Position": 22882,
"Reference_Base": "T",
"Alternate_Base": "G",
"Variant": "22882T>G",
"Amino_Acid_Position": 440,
"Reference_Amino_Acid": "N (Asn)",
"Alternate_Amino_acid": "K (Lys)",
"AA_Change": "N440K",
"Type_of_Mutation": "Escape mutant",
"VoCs_VoIs": "None",
"VoCs_VoIs_link": "None",
"VoCs_VoIs_Aliases": "None",
"VoCs_VoIs_Aliases_link": "None",
"VoCs_VoIs_Description": "None",
"PROTEIN_NAME": "Spike glycoprotein",
"UNIPROT_PROTEIN_ID": "P0DTC2",
"UNIPROT_PROTEIN_ID_LINK": "https:\/\/www.uniprot.org\/uniprot\/P0DTC2#family_and_domains",
"PROTEIN_LENGTH": "1273 amino acids",
"Protein_Description": "Spike protein is one of the structural proteins of SARS-CoV-2. The monomeric protein consists of one large ectodomain, a single-pass transmembrane anchor, and a short intracellular tail at C-terminus. It encompasses 22 glycosylation sites. S protein cleaves into two subunits namely S1 and S2 following receptor recognition. Receptor Binding Domain (RBD) in S1 subunit plays a major role in ACE2 receptor binding.",
"Protein_Domain": "Receptor Binding Domain (RBD) of SARS-CoV-2. The SARS-CoV-2 RBD has a twisted five-stranded antiparallel \u03b2 sheet (\u03b21, \u03b22, \u03b23, \u03b24 and \u03b27) with short connecting helices and loops that form the core. Between the \u03b24 and \u03b27 strands in the core, there is an extended insertion containing the short \u03b25 and \u03b26 strands, \u03b14 and \u03b15 helices and loops. ",
"Domain_position": "SARS-CoV-2 RBD (residues Arg319\u2013Phe541)",
"Function_of_the_Domain": "Receptor Binding Domain is a vital immunogenic fragment in the Spike protein of SARS-CoV-2 virus that binds to specific endogenous receptors in the host. SARS-CoV-2 gains entry and causes infection in humans by binding to ACE2 receptor.",
"Epitope_Type": "Linear peptide",
"IEDB_Reference_B_cell_epitope_Sequence": "KLPDDFTGCVIAWNSNNLDS (424-443)##LPDDFTGCVIAWNSNNLD (425-442)## VIAWNSNNLDSKVGGNYN (433-450)##IAWNSNNLDSKVGGNYNYLY (434-453)",
"B_cell_Epitope_ID": "1309501##1087618##1087772## 1309490",
"IEDB_Antigen_Accession": "QII57161.1##QHD43416.1##QII57161.1##QHD43416.1",
"IEDB_linkout": "",
"Predicted_B_cell_Epitopes": "LPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERD (425-467)##PDDFTGCVIAWNSNN (426-440)##DDFTGCVIAWNSNNL (427-441)##GCVIAWNSNNLDSKV (431-445)##WNSNNLDSKVGGNYN (436-450)##NLDSKVGGNY (440-449)",
"Predicted_B_cell_epitope_Binding_affinity": "1074979##1310707##1069293##1310437##1310945##1075002",
"Predicted_T_cell_Epitopes": "YP_009724390.1##QKE11719.1##QHD43416.1##QKE11719.1##QKE11719.1##YP_009724390.1",
"Predicted_T_cell_epitope_Binding_affinity": "",
"Antibody_Name": "REGN10987\/Imdevimab",
"Antibody_Category_and_Description": "Class III Antibody. hNAbs that bind outside the ACE2 binding site and recognize both \u201cup\u201d and \u201cdown\u201d RBD conformations. Casirivimab and Imdevimab are human immunoglobulin G-1 (IgG1) monoclonal antibodies produced by recombinant DNA technology in the lab. Monoclonal antibodies are proteins that mimic the immune system\u2019s ability to fight off harmful pathogens such as viruses. Casirivimab and Imdevimab are monoclonal antibodies that are specifically directed against the spike protein of SARS-CoV-2, designed to block the virus\u2019 attachment and entry into human cells. Thanks to its specific engineering of two neutralising antibodies which bind to different parts of the virus spike, the Casirivimab and Imdevimab cocktail remains efficacious against widest spread variants and reduces the risk of losing its neutralisation potency against new emerging variants.",
"ABCD_(AntiBodies_Chemically_Defined)_Database_ID": "ABCD_AT869",
"Antibody_linkout_": "https:\/\/web.expasy.org\/abcd\/ABCD_AT869",
"Antibody_Details": "",
"Study_Type": "Computational predictions and Experimental methods",
"Details_of_the_study": "Generation of replication defective VSV pseudovirus expressing SARS- CoV-2 spike protein followed by pseudovirus neutralization assays. Mutations predicted to be potential escape variations were tested against a panel of 144 mAbs isolated from patients recovered from SARS-CoV2 infection as well against clinical stage antibodies.##>2-fold reduction of RBD binding was observed corresponding to this mutation.",
"RefGene_Function": "Protein Coding Region",
"Variation_Type": "Nonsynonymous SNV",
"SIFT_Score": 0.73,
"SIFT_Prediction": "Tolerated",
"GERP": -3.3,
"PhyloP": 0.135937,
"PhastCons": 0,
"Uniprot_Domains": "Disulf_bond",
"UNIPROT_Disulphite_Bond": "BetaCoV_S1-CTD",
"UNIPROT_glyphos": "NA",
"UNIPROT_Transmembrane": "NA",
"IEDB_B-Cell_Epitopes": "Surface glycoprotein_IAWNSNNLDSK",
"IEDB_CD4_Epitopes": "NA",
"IEDB_cd4Epitope_Score": "NA",
"IEDB_CD8_Epitopes": "NA",
"IEDB_cd8Epitope_Score": "NA",
"MPDI_Potential_Immunogenic_Regions": "NA",
"MPDI_Potential_Immunodominant_Epitopes": "NA",
"ARTIC_Primers": "nCoV-2019_75_RIGHT",
"RT-PCR_Primers\/Probes": "NA",
"Sequencing_Error_Sites": "NA",
"Homoplasic_Positions": "NA",
"Hypermutable_Sites": "NA",
"Global_Variant_Frequency": 0.00206889,
"Geographical_Variant_Frequency": "Africa(0.00600236)##Asia(0.0153999)##Europe(0.000959122)##NorthAmerica(0.00114642)##Oceania(0.000559884)##SouthAmerica(0.00306081)",
"Reference": "Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. H., Choudhary, M. C., Dingens, A. S., et al. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. doi:10.1101\/2020.11.30.405472.",
"Reference_Link": "https:\/\/science.sciencemag.org\/content\/371\/6531\/850",
"hc-key": "af,as,eu,na,oc,sa",
"value": "0.00600236,0.0153999,0.000959122,0.00114642,0.000559884,0.00306081",
"Experiment_type": "Mutations in isolation",
"Neutralization_quantification": "REGN10987-0.565",
"Ensembl_Gene_ID": "ENSSASG00005000004",
"Ensembl_Gene_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Gene\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"Ensembl_Transcript_ID": "ENSSAST00005000004.1",
"Ensembl_Transcript_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Transcript\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"CDS_Position": 1320,
"Codons": "aaT\/aaG",
"Ensembl_Variant_ID": "MN908947.3:22882:T:G",
"Variant_Location": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Location\/View?db=core;r=MN908947.3:22872-22892",
"HGVS_Nomenclature": "None",
"Variant_Population_genetics": "None",
"Variant_Sample_Genotype": "None",
"Antibody_Generation": "Publicly available antibody variable domain sequences were acquired for REGN10933, REGN10987, and LY-CoV016 (also known as JS016, LY3832479, or CB6). Recombinant antibodies were cloned and produced by Genscript. Specifically, antibody variable domains were cloned with the human IgG1 heavy chain and human IgK (REGN10933 and LY-CoV016) or human IgL2 (REGN10987) constant regions into pcDNA3.4 vector, and transfected into HD 293F cells maintained at 37\u00b0C with 8% CO2 on an orbital shaker.",
"SARS-CoV-2_Mutants_Generation": "",
"Antibody_Binding_escape_Profile": "Antibody selection experiments were performed in biological duplicate using a deep mutational scanning (mutational antigenic profiling) approach"
},
{
"_id": {
"$oid": "613deea3d2b575ce3b35814d"
},
"Gene": "S",
"NCBI_Gene_ID": 43740568,
"Gene_ID_Link": "https:\/\/www.ncbi.nlm.nih.gov\/gene\/43740568",
"Gene_Location": "NC_045512.2:21563-25384",
"Gene_Location_link": "https:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?hgtgroup_map_close=0&hgtgroup_genes_close=0&hgtgroup_uniprot_close=0&hgtgroup_immu_close=0&hgtgroup_rna_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0&hgsid=950344573_A9vhn3kpWNAevyURQKIFZD7Av59E&position=NC_045512.2%3A21563-25384&hgt.positionInput=NC_045512.2%3A21563-25384&goButton=go&db=wuhCor1&c=NC_045512v2&l=265&r=21555&pix=950&dinkL=2.0&dinkR=2.0",
"Variant_Position": 22882,
"Reference_Base": "T",
"Alternate_Base": "G",
"Variant": "22882T>G",
"Amino_Acid_Position": 440,
"Reference_Amino_Acid": "N (Asn)",
"Alternate_Amino_acid": "K (Lys)",
"AA_Change": "N440K",
"Type_of_Mutation": "Resistant to Abs",
"VoCs_VoIs": "None",
"VoCs_VoIs_link": "None",
"VoCs_VoIs_Aliases": "None",
"VoCs_VoIs_Aliases_link": "None",
"VoCs_VoIs_Description": "None",
"PROTEIN_NAME": "Spike glycoprotein",
"UNIPROT_PROTEIN_ID": "P0DTC2",
"UNIPROT_PROTEIN_ID_LINK": "https:\/\/www.uniprot.org\/uniprot\/P0DTC2#family_and_domains",
"PROTEIN_LENGTH": "1273 amino acids",
"Protein_Description": "Spike protein is one of the structural proteins of SARS-CoV-2. The monomeric protein consists of one large ectodomain, a single-pass transmembrane anchor, and a short intracellular tail at C-terminus. It encompasses 22 glycosylation sites. S protein cleaves into two subunits namely S1 and S2 following receptor recognition. Receptor Binding Domain (RBD) in S1 subunit plays a major role in ACE2 receptor binding.",
"Protein_Domain": "Receptor Binding Domain (RBD) of SARS-CoV-2. The SARS-CoV-2 RBD has a twisted five-stranded antiparallel \u03b2 sheet (\u03b21, \u03b22, \u03b23, \u03b24 and \u03b27) with short connecting helices and loops that form the core. Between the \u03b24 and \u03b27 strands in the core, there is an extended insertion containing the short \u03b25 and \u03b26 strands, \u03b14 and \u03b15 helices and loops. ",
"Domain_position": "SARS-CoV-2 RBD (residues Arg319\u2013Phe541)",
"Function_of_the_Domain": "Receptor Binding Domain is a vital immunogenic fragment in the Spike protein of SARS-CoV-2 virus that binds to specific endogenous receptors in the host. SARS-CoV-2 gains entry and causes infection in humans by binding to ACE2 receptor.",
"Epitope_Type": "Linear peptide",
"IEDB_Reference_B_cell_epitope_Sequence": "KLPDDFTGCVIAWNSNNLDS (424-443)##LPDDFTGCVIAWNSNNLD (425-442)## VIAWNSNNLDSKVGGNYN (433-450)##IAWNSNNLDSKVGGNYNYLY (434-453)",
"B_cell_Epitope_ID": "1309501##1087618##1087772## 1309490",
"IEDB_Antigen_Accession": "QII57161.1##QHD43416.1##QII57161.1##QHD43416.1",
"IEDB_linkout": "",
"Predicted_B_cell_Epitopes": "LPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERD (425-467)##PDDFTGCVIAWNSNN (426-440)##DDFTGCVIAWNSNNL (427-441)##GCVIAWNSNNLDSKV (431-445)##WNSNNLDSKVGGNYN (436-450)##NLDSKVGGNY (440-449)",
"Predicted_B_cell_epitope_Binding_affinity": "1074979##1310707##1069293##1310437##1310945##1075002",
"Predicted_T_cell_Epitopes": "YP_009724390.1##QKE11719.1##QHD43416.1##QKE11719.1##QKE11719.1##YP_009724390.1",
"Predicted_T_cell_epitope_Binding_affinity": "",
"Antibody_Name": "C135",
"Antibody_Category_and_Description": "Isotype - Mouse IgG1 ; Anti-Human CD4. Class II antibody. hNAbs that overlap with the ACE2 binding site and recognize both \u201cup\u201d and \u201cdown\u201d RBD conformations",
"ABCD_(AntiBodies_Chemically_Defined)_Database_ID": "ABCD_AT512",
"Antibody_linkout_": "https:\/\/web.expasy.org\/abcd\/ABCD_AT512",
"Antibody_Details": "",
"Study_Type": "Computational Prediction",
"Details_of_the_study": "",
"RefGene_Function": "Protein Coding Region",
"Variation_Type": "Nonsynonymous SNV",
"SIFT_Score": 0.73,
"SIFT_Prediction": "Tolerated",
"GERP": -3.3,
"PhyloP": 0.135937,
"PhastCons": 0,
"Uniprot_Domains": "Disulf_bond",
"UNIPROT_Disulphite_Bond": "BetaCoV_S1-CTD",
"UNIPROT_glyphos": "NA",
"UNIPROT_Transmembrane": "NA",
"IEDB_B-Cell_Epitopes": "Surface glycoprotein_IAWNSNNLDSK",
"IEDB_CD4_Epitopes": "NA",
"IEDB_cd4Epitope_Score": "NA",
"IEDB_CD8_Epitopes": "NA",
"IEDB_cd8Epitope_Score": "NA",
"MPDI_Potential_Immunogenic_Regions": "NA",
"MPDI_Potential_Immunodominant_Epitopes": "NA",
"ARTIC_Primers": "nCoV-2019_75_RIGHT",
"RT-PCR_Primers\/Probes": "NA",
"Sequencing_Error_Sites": "NA",
"Homoplasic_Positions": "NA",
"Hypermutable_Sites": "NA",
"Global_Variant_Frequency": 0.00206889,
"Geographical_Variant_Frequency": "Africa(0.00600236)##Asia(0.0153999)##Europe(0.000959122)##NorthAmerica(0.00114642)##Oceania(0.000559884)##SouthAmerica(0.00306081)",
"Reference": "Barnes, C. O., Jette, C. A., Abernathy, M. E., Dam, K.-M. A., Esswein, S. R., Gristick, H. B., Malyutin, A. G., Sharaf, N. G., Huey-Tubman, K. E., Lee, Y. E., Robbiani, D. F., Nussenzweig, M. C., West, A. P., & Bjorkman, P. J. (2020). Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. In Cold Spring Harbor Laboratory (p. 2020.08.30.273920). https:\/\/doi.org\/10.1101\/2020.08.30.27392",
"Reference_Link": "https:\/\/www.biorxiv.org\/content\/10.1101\/2020.08.30.273920v1.full",
"hc-key": "af,as,eu,na,oc,sa",
"value": "0.00600236,0.0153999,0.000959122,0.00114642,0.000559884,0.00306081",
"Experiment_type": "Mutations in isolation",
"Neutralization_quantification": "KD = NA",
"Ensembl_Gene_ID": "ENSSASG00005000004",
"Ensembl_Gene_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Gene\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"Ensembl_Transcript_ID": "ENSSAST00005000004.1",
"Ensembl_Transcript_ID_link": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Transcript\/Summary?db=core;g=ENSSASG00005000004;r=MN908947.3:21563-25384;t=ENSSAST00005000004;tl=teEdDKlYVhAur3jY-242",
"CDS_Position": 1320,
"Codons": "aaT\/aaG",
"Ensembl_Variant_ID": "MN908947.3:22882:T:G",
"Variant_Location": "https:\/\/covid-19.ensembl.org\/Sars_cov_2\/Location\/View?db=core;r=MN908947.3:22872-22892",
"HGVS_Nomenclature": "None",
"Variant_Population_genetics": "None",
"Variant_Sample_Genotype": "None",
"Antibody_Generation": "Crystallization trials were carried out at room temperature using the sitting drop vapor diffusion method. Crystals were obtained in 0.2 M ammonium sulfate, 20% w\/v PEG 3350 (C102 Fab), 0.2 M sodium citrate tribasic, 20% w\/v PEG 3350 (C102-RBD), 0.2 M lithium sulfate monohydrate, 20% w\/v PEG 3350 (C002 Fab), 0.04 M potassium phosphate, 16% w\/v PEG 8000, 20% v\/v glycerol (C135 Fab), 0.2 M ammonium citrate pH 5.1, 20% PEG 3350 (C121 Fab), or 0.2 M sodium tartrate dibasic dihydrate pH 7.3, 20 % w\/v PEG 3350 (C110 Fab). A C135 Fab crystal was directly looped and cryopreserved in liquid nitrogen.",
"SARS-CoV-2_Mutants_Generation": "Constructs encoding the SARS-CoV-2 RBD from GenBank MN985325.1 (residues 331-524 with C-terminal octa-His tag and AviTag) and mutant RBDs were generated. Fabs and IgGs were expressed, purified, and stored",
"Antibody_Binding_escape_Profile": "Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D"
}
],
"error": null
}
}
{
...,
"datasetResponses": null
}