Structure of the Sars-Cov-2 Spike Glycoprotein in complex with the S309 Neutralizing antibody Fab Fragment (Open State)
PDB | 6wpt |
Species | HOMO SAPIENS |
Method | ELECTRON MICROSCOPY |
Resolution | 3.7Å |
Number of Fvs | 2 |
In complex | True |
Light chain type | Kappa |
Has constant region | False |
Affinity | NA |
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Display options: |
This PDB has 2 Fv(s).
Fv Details | |
---|---|
Heavy chain | H |
Light chain | L |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV3 |
Species | HOMO SAPIENS |
In complex? | True |
scFv? | False |
Has constant domain? | False |
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 | 100D | 100E | 100F | 100G | 100H | 100I | 100J | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Q | V | Q | L | V | Q | S | G | A | E | V | K | K | P | G | A | S | V | K | V | S | C | K | A | S | G | Y | P | F | T | S | Y | G | I | S | W | V | R | Q | A | P | G | Q | G | L | E | W | M | G | W | I | S | T | Y | N | G | N | T | N | Y | A | Q | K | F | Q | G | R | V | T | M | T | T | D | T | S | T | T | T | G | Y | M | E | L | R | R | L | R | S | D | D | T | A | V | Y | Y | C | A | R | D | Y | T | R | G | A | W | F | G | E | S | L | I | G | G | F | D | N | 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 | 30A | 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 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
E | I | V | L | T | Q | S | P | G | T | L | S | L | S | P | G | E | R | A | T | L | S | C | R | A | S | Q | T | V | S | S | T | S | L | A | W | Y | Q | Q | K | P | G | Q | A | P | R | L | L | I | Y | G | A | S | S | R | A | T | G | I | P | D | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | S | R | L | E | P | E | D | F | A | V | Y | Y | C | Q | Q | H | D | T | S | L | T | F | G | G | G | T | K | V | E | I | K |
Antigen Details | |
---|---|
Antigen chains | C |
Antigen type | protein |
Antigen name | sars-cov-2 spike glycoprotein |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYPFTSY |
CDRH2 | STYNGN |
CDRH3 | DYTRGAWFGESLIGGFDN |
CDRL1 | RASQTVSSTSLA |
CDRL2 | GASSRAT |
CDRL3 | QQHDTSLT |
Orientation Angles (from ABangle) | |
---|---|
HL | -64.0° |
HC1 | 70.89° |
HC2 | 117.85° |
LC1 | 122.85° |
LC2 | 82.04° |
dc | 16.13Å |
Fv Details | |
---|---|
Heavy chain | D |
Light chain | E |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV3 |
Species | HOMO SAPIENS |
In complex? | True |
scFv? | False |
Has constant domain? | False |
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 | 100D | 100E | 100F | 100G | 100H | 100I | 100J | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Q | V | Q | L | V | Q | S | G | A | E | V | K | K | P | G | A | S | V | K | V | S | C | K | A | S | G | Y | P | F | T | S | Y | G | I | S | W | V | R | Q | A | P | G | Q | G | L | E | W | M | G | W | I | S | T | Y | N | G | N | T | N | Y | A | Q | K | F | Q | G | R | V | T | M | T | T | D | T | S | T | T | T | G | Y | M | E | L | R | R | L | R | S | D | D | T | A | V | Y | Y | C | A | R | D | Y | T | R | G | A | W | F | G | E | S | L | I | G | G | F | D | N | 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 | 30A | 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 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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E | I | V | L | T | Q | S | P | G | T | L | S | L | S | P | G | E | R | A | T | L | S | C | R | A | S | Q | T | V | S | S | T | S | L | A | W | Y | Q | Q | K | P | G | Q | A | P | R | L | L | I | Y | G | A | S | S | R | A | T | G | I | P | D | R | F | S | G | S | G | S | G | T | D | F | T | L | T | I | S | R | L | E | P | E | D | F | A | V | Y | Y | C | Q | Q | H | D | T | S | L | T | F | G | G | G | T | K | V | E | I | K |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | sars-cov-2 spike glycoprotein |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GYPFTSY |
CDRH2 | STYNGN |
CDRH3 | DYTRGAWFGESLIGGFDN |
CDRL1 | RASQTVSSTSLA |
CDRL2 | GASSRAT |
CDRL3 | QQHDTSLT |
Orientation Angles (from ABangle) | |
---|---|
HL | -64.98° |
HC1 | 70.55° |
HC2 | 118.0° |
LC1 | 122.87° |
LC2 | 81.67° |
dc | 16.19Å |
Occurences of this structure in other OPIG databases.
Ab_or_Nb | Ab |
Binds_to | SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV1 |
Does_not_bind_to | None |
Neutralising_vs | SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV1 |
Not_Neutralising_vs | None |
Protein_and_Epitope | S; RBD |
Origin | B-cells; SARS-CoV1 Human Patient |
VH_or_VHH | QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVSS |
VL | EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIK |
Heavy_V_Gene | IGHV1-18 (Human) |
Heavy_J_Gene | IGHJ4 (Human) |
Light_V_Gene | IGKV3-20 (Human) |
Light_J_Gene | IGKJ4 (Human) |
CDRH3 | ARDYTRGAWFGESLIGGFDN |
CDRL3 | QQHDTSLT |
Structures | https://www.rcsb.org/structure/6WPS;https://www.rcsb.org/structure/6WPT;https://www.rcsb.org/structure/6WS6;https://www.rcsb.org/structure/7JX3;https://www.rcsb.org/structure/7L0N;https://www.rcsb.org/structure/7BEP;https://www.rcsb.org/structure/7R6W;https://www.rcsb.org/structure/7R6X;https://www.rcsb.org/structure/7SOB;https://www.rcsb.org/structure/7TLY;https://www.rcsb.org/structure/7TLZ;https://www.rcsb.org/structure/7TM0;https://www.rcsb.org/structure/7TN0 |
ABB_Homology_Model | None |
Sources | Dora Pinto et al., 2020 (https://www.nature.com/articles/s41586-020-2349-y);Luca Piccoli et al., 2020 (https://www.cell.com/cell/fulltext/S0092-8674(20);Wanwisa Dejnirattisai et al., 2021 (https://www.cell.com/cell/fulltext/S0092-8674(21);Tyler Starr et al., 2021 (https://www.nature.com/articles/s41586-021-03807-6);Dhiraj Mannar et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473380v1);Daniel Sheward et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473354v1);Laura VanBlargan et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.15.472828v1);Garrett Rappazzo et al., 2021 (https://www.science.org/doi/10.1126/science.abf4830);Tongqing Zhou et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.27.474307v1);Matthew McCallum et al., 2021 (https://dx.doi.org/10.1126/science.abn8652);Bin Ju et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.19.476892v1);Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1) |
Date_Added | May 4, 2020 |
Last_Updated | Mar 4, 2022 |
Update_Description | 28th May: Added sequence and crystal structure information. 15th June: Added 6ws6 structure. 16th October: Added more PDB structures. 28th Feb: Added 7L0N and new reference. 11th March: Added 7BEP. 24th July '21: Added new PDB structure and reference. 2nd Dec '21: Added new PDB structure. 28th Dec '21: Added Omicron-BA1 neturalisation data. 31st Jan '22: Added new neutralisation studies. 4th Mar '22: Added structures of S309 bound to Omicron-BA1 and Omicron-BA2 data. |
Notes_Following_Up | Extra variant binding data in Starr et al. Complete |
TheraSAbDab | link |
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]