Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5243 |
| PDBID: | 7UZ8 |
| Chains: | MN_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Mus musculus |
| Method: | EM |
| Resolution (Å): | 3.10 |
| Reference: | 10.1016/j.immuni.2022.10.019 |
| Antibody | |
| Antibody: | M8a-31 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: M
Mutation: NULL
| >7UZ8_M|Chain D[auth H], F[auth M], H[auth P]|M8a-31 Fab heavy chain|Mus musculus (10090) EVQLKQSVAELVRPGASVKVSCTASGFNIKNIYMHWVKQRPEQGLDWIGRIDPANGNSRYAPKFQDKATITADTSSNTAYLQLSSLTSEDTAIYYCADEGWGFANWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH |
Light Chain: N
Mutation: NULL
| >7UZ8_N|Chain E[auth L], G[auth N], I[auth Q]|M8a-31 Fab light chain|Mus musculus (10090) DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKVGQPPKLLIYWASTRDPGVPDRFTGSGFGTDFTLTISSVQAEDLAVYYCQNDYSYPLTFGAGTKVELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: B
Mutation: A67V/A93I/F140D/R208R/209E/210P/211E/G336D/S368L/S370P/S372F/K414N/N437K/G443S/S474N/T475K/E481A/Q490R/G493S/Q495R/N498Y/Y502H/T544K/D611G/H652Y/N676K/P678H/R679A/T758K/P790Y/K811P/Q850K/G886P/I893P/S936P/V948H/L963K/N975F/R980P/L981P
| >7UZ8_B|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| M: GLU1 VAL2 GLY27 PHE28 LYS35 ASN36 ILE37 TYR38 ASP57 ASP106 GLU107 GLY108 TRP109 ALA116 ASN117 N: ASN31 SER32 GLY33 ASN34 GLN35 LYS36 TYR38 LEU52 TYR55 TRP56 THR66 ARG67 ASP68 PRO69 GLY70 PRO72 B: TYR369 ASN370 LEU371 ALA372 PHE374 PHE375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 ASP389 LEU390 CYS391 PHE392 VAL407 ARG408 ALA411 PRO412 GLY413 ASP427 ASP428 PHE429 THR430 LEU517 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
