Structure Viewer: 7c01

>   Structure details

Molecular Basis For a Potent Human Neutralizing antibody Targeting Sars-Cov-2 Rbd

PDB7c01
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.88Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
AffinityNA
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>   Fv information

This PDB has 2 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C A A S G F T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T F Y A D S V K G R F T I S R D N S M N T L F L Q M N S L R A E D T A V Y Y C A R V L P M Y G D Y L D Y W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107
D I V M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P P E Y T F G Q G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namesars-cov-2 spike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTVSSN
CDRH2YSGGS
CDRH3VLPMYGDYLDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTPPEYT

Orientation Angles (from ABangle)
HL-63.34°
HC171.85°
HC2118.79°
LC1121.16°
LC283.2°
dc16.06Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C A A S G F T V S S N Y M S W V R Q A P G K G L E W V S V I Y S G G S T F Y A D S V K G R F T I S R D N S M N T L F L Q M N S L R A E D T A V Y Y C A R V L P M Y G D Y L D Y W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107
D I V M T Q S P S S L S A S V G D R V T I T C R A S Q S I S R Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A T Y Y C Q Q S Y S T P P E Y T F G Q G T K L E I K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namesars-cov-2 spike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTVSSN
CDRH2YSGGS
CDRH3VLPMYGDYLDY
CDRL1RASQSISRYLN
CDRL2AASSLQS
CDRL3QQSYSTPPEYT

Orientation Angles (from ABangle)
HL-64.6°
HC171.11°
HC2119.07°
LC1119.78°
LC282.92°
dc16.15Å
>   Occurences in auxilliary databases

Occurences of this structure in other OPIG databases.

>   CoVAbDab entry
Ab_or_Nb Ab
Binds_to SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta (weak);SARS-CoV2_Gamma (weak);SARS-CoV2_Delta
Does_not_bind_to SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV2_Omicron-BA2.11;SARS-CoV2_Omicron-BA2.12.1;SARS-CoV2_Omicron-BA2.4;SARS-CoV2_Omicron-BA2.5
Neutralising_vs SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta (weak);SARS-CoV2_Gamma (weak);SARS-CoV2_Delta
Not_Neutralising_vs SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV2_Omicron-BA2.11;SARS-CoV2_Omicron-BA2.12.1;SARS-CoV2_Omicron-BA2.4;SARS-CoV2_Omicron-BA2.5
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV2_WT Human Patient
VH_or_VHH EVQLVESGGGLVQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSMNTLFLQMNSLRAEDTAVYYCARVLPMYGDYLDYWGQGTLVTVSS
VL DIVMTQSPSSLSASVGDRVTITCRASQSISRYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPPEYTFGQGTKLEIK
Heavy_V_Gene IGHV3-66 (Human)
Heavy_J_Gene IGHJ4 (Human)
Light_V_Gene IGKV1-39 (Human)
Light_J_Gene IGKJ2 (Human)
CDRH3 ARVLPMYGDYLDY
CDRL3 QQSYSTPPEYT
Structures https://www.rcsb.org/structure/7C01
ABB_Homology_Model None
Sources Rui Shi et al., 2020 (https://www.nature.com/articles/s41586-020-2381-y_reference.pdf);
NCBI (https://www.ncbi.nlm.nih.gov/nuccore/MT470194);
NCBI (https://www.ncbi.nlm.nih.gov/nuccore/MT4701945);
Daniel Sheward et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473354v1);
Delphine Planas et al., 2021 (https://www.nature.com/articles/s41586-021-03777-9);
Laura VanBlargan et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.15.472828v1);
Delphine Planas et al., 2021 (https://www.nature.com/articles/d41586-021-03827-2);
Lihong Liu et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.14.472719v3);
Xun Wang et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.24.474138v1);
Takuya Tada et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.28.474369v1);
Tongqing Zhou et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.27.474307v1);
Matthew McCallum et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.28.474380v1);
Franck Touret et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.01.474639v1);
Celine Boschi et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.03.474769v1);
Bin Ju et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.19.476892v1);
Hang Ma et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.25.482049v1);
Hao Zhou et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.15.480166v2);
Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1);
Daichi Yamasoba et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.05.03.490409v1)
Date_Added May 28, 2020
Last_Updated Jun 14, 2022
Update_Description Added therapeutic relevance. 28th Dec '21: Added variant neutralisation data. 31st Jan '22: Added new neutralisation studies. 4th Mar '22: Added omicron BA2 data
Notes_Following_Up Therapeutic mAb Etesevimab. Also known as LY-CoV016. Debate as to extent of Beta and Gamma variant neutralisation. Complete

TheraSAbDab link
>   Downloads

Additional links and files for download: see help for more details.

Chothia-numbered structure Download
IMGT-numbered structure Download
Non-annotated structure from the PDB Download
Summary file for this antibody Download

SAbDab papers

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

Dunbar, J., Krawczyk, K. et al. (2014) SAbDab: the Structural Antibody Database. Nucleic Acids Res. 42(D1):D1140-D1146 [link]

Thera-SAbDab paper

Raybould, M.I.J., Marks, C. et al (2020) Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48(D1):D383-D388. [link]

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