Structure Viewer: 6xdg

>   Structure details

complex of Sars-Cov-2 Receptor Binding Domain with the Fab Fragments of Two Neutralizing antibodies

PDB6xdg
SpeciesMUS MUSCULUS; HOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.9Å
Number of Fvs2
In complexTrue
Light chain typeKappa,Lambda
Has constant regionTrue
AffinityNA
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>   Fv information

This PDB has 2 Fv(s).

>   B/D
Fv Details
Heavy chainB
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMUS MUSCULUS
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 52A 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
Q V Q L V E S G G G L V K P G G S L R L S C A A S G F T F S D Y Y M S W I R Q A P G K G L E W V S Y I T Y S G S T I Y Y A D S V K G R F T I S R D N A K S S L Y L Q M N S L R A E D T A V Y Y C A R D R G T T M V P F 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q M T Q S P S S L S A S V G D R V T I T C Q A S Q D I T N Y L N W Y Q Q K P G K A P K L L I Y A A S N L E T G V P S R F S G S G S G T D F T F T I S G L Q P E D I A T Y Y C Q Q Y D N L P L T F G G G T K V E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFEQKLISEEDLGGEQKLISEEDLHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2TYSGST
CDRH3DRGTTMVPFDY
CDRL1QASQDITNYLN
CDRL2AASNLET
CDRL3QQYDNLPLT

Orientation Angles (from ABangle)
HL-57.57°
HC174.14°
HC2116.57°
LC1118.52°
LC284.71°
dc16.45Å
>   C/A
Fv Details
Heavy chainC
Light chainA
Heavy subgroupIGHV3
Light subgroupIGLV2
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 52A 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
Q V Q L V E S G G G V V Q P G R S L R L S C A A S G F T F S N Y A M Y W V R Q A P G K G L E W V A V I S Y D G S N K Y Y A D S V K G R F T I S R D N S K N T L Y L Q M N S L R T E D T A V Y Y C A S G S D Y G D Y L L V Y W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 30C 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 96 97 98 99 100 101 102 103 104 105 106 107
Q S A L T Q P A S V S G S P G Q S I T I S C T G T S S D V G G Y N Y V S W Y Q Q H P G K A P K L M I Y D V S K R P S G V S N R F S G S K S G N T A S L T I S G L Q S E D E A D Y Y C N S L T S I S T W V F G G G T K L T V L

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFEQKLISEEDLGGEQKLISEEDLHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTFSNY
CDRH2SYDGSN
CDRH3GSDYGDYLLVY
CDRL1TGTSSDVGGYNYVS
CDRL2DVSKRPS
CDRL3NSLTSISTWV

Orientation Angles (from ABangle)
HL-59.73°
HC173.88°
HC2120.09°
LC1116.72°
LC281.18°
dc16.39Å
>   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_Gamma;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;SARS-CoV1
Protein_and_Epitope S; RBD
Origin B-cells; Transgenic Mouse (VelocImmune)
VH_or_VHH QVQLVESGGGLVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSYITYSGSTIYYADSVKGRFTISRDNAKSSLYLQMNSLRAEDTAVYYCARDRGTTMVPFDYWGQGTLVTVSS
VL DIQMTQSPSSLSASVGDRVTITCQASQDITNYLNWYQQKPGKAPKLLIYAASNLETGVPSRFSGSGSGTDFTFTISGLQPEDIATYYCQQYDNLPLTFGGGTKVEIK
Heavy_V_Gene IGHV3-11 (Human)
Heavy_J_Gene IGHJ4 (Human)
Light_V_Gene IGKV1-33 (Human)
Light_J_Gene IGKJ4 (Human)
CDRH3 ARDRGTTMVPFDY
CDRL3 QQYDNLPLT
Structures https://www.rcsb.org/structure/6XDG
ABB_Homology_Model None
Sources Johanna Hansen et al., 2020 (https://science.sciencemag.org/content/early/2020/06/15/science.abd0827);
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);
Lauren 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);
Nitin Hingankar et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.25.474152v1);
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 (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);
Hirofumi Ohashi et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.27.482147v1);
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);
Sebastian Fiedler et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.03.478946v2);
Daichi Yamasoba et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.05.03.490409v1)
Date_Added Jun 21, 2020
Last_Updated Jun 14, 2022
Update_Description 11th Nov: Added therapeutic relevance; 16th Nov: Clarified sequence origin by cross-referencing patent; 28th Dec '21: Added variant binding/neutralisation data; 31st Jan '22: Added extra neutralisation studies; 4th Mar '22: Added Omicron BA2 neutralisation data. 14th Jun '22: Added new reference and omicron neutralisation data.
Notes_Following_Up Therapeutic mAb Casirivimab/Nepuvibart. Debate as to neutralisation strength versus Beta and Gamma variants. Also may very weakly neutralise omicron variants (see Ohashi et al). Complete

TheraSAbDab link
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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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