7KKK
Sars-cov-2 spike in complex with neutralizing nanobody nb6
PDB DOI: 10.2210/pdb7kkk/pdb
Classification: VIRAL PROTEIN/IMMUNE SYSTEM Organism(s): Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct
Deposited: 2020-10-27 Deposition Author(s): Anand, A.A. , Azumaya, C.M. , Barile-Hill, A.W. , Barsi-Rhyne, B. , Belyy, V. , Billesboelle, C.B. , Boone, M. , Brilot, A.F. , Bulkley, D. , Chio, C.M. , Chio, U.S. , Desphande, I. , Dickinson, S. , Diwanji, D. , Dobzinski, N. , Faust, B.F. , Garcia-Sastre, A. , Gupta, M. , Gupta, S. , Hoppe, N. , Jin, M. , Kratochvil, H.T. , Krogan, N.J. , Leon, K. , Li, F. , Liang, J. , Liu, Y. , Liu, Y. , Manglik, A. , Merz, G.E. , Moss, F. , Nguyen, H.C. , Nock, S. , Ott, M. , Pospiech, T. , Pourmal, S. , Puchades, C. , Qcrg Structural Biology Consortium , Ralston, C.Y. , Rezelj, V. , Rizo, A.N. , Sangwan, S. , Saunders, R.A. , Schaefer, K. , Schoof, M.S. , Simoneau, C.R. , Smith, A.M. , Sun, M. , Swaney, D.L. , Thompson, M.C. , Trenker, R. , Vignuzzi, M. , Walter, P. , White, K.M. , Zha, B.S. , Zhang, K. , Zimanyi, M.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.03 Å
Sars-cov-2 spike in complex with neutralizing nanobody nb6
Anand, A.A. , Azumaya, C.M. , Barile-Hill, A.W. , Barsi-Rhyne, B. , Belyy, V. , Billesboelle, C.B. , Boone, M. , Brilot, A.F. , Bulkley, D. , Chio, C.M. , Chio, U.S. , Desphande, I. , Dickinson, S. , Diwanji, D. , Dobzinski, N. , Faust, B.F. , Garcia-Sastre, A. , Gupta, M. , Gupta, S. , Hoppe, N. , Jin, M. , Kratochvil, H.T. , Krogan, N.J. , Leon, K. , Li, F. , Liang, J. , Liu, Y. , Liu, Y. , Manglik, A. , Merz, G.E. , Moss, F. , Nguyen, H.C. , Nock, S. , Ott, M. , Pospiech, T. , Pourmal, S. , Puchades, C. , Qcrg Structural Biology Consortium , Ralston, C.Y. , Rezelj, V. , Rizo, A.N. , Sangwan, S. , Saunders, R.A. , Schaefer, K. , Schoof, M.S. , Simoneau, C.R. , Smith, A.M. , Sun, M. , Swaney, D.L. , Thompson, M.C. , Trenker, R. , Vignuzzi, M. , Walter, P. , White, K.M. , Zha, B.S. , Zhang, K. , Zimanyi, M.
Primary Citation of Related Structures: 7KKK
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Spike glycoprotein | A | 1288 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
| Spike glycoprotein | C | 1288 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
| Spike glycoprotein | E | 1288 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK |
| Synthetic nanobody Nb6 | B | 119 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | QVQLVESGGGLVQAGGSLRLSCAASGIIFGRNAMGWYRQAPGKERELVAGITRRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADPASPAPGDYWGQGTQVTVSS |
| Synthetic nanobody Nb6 | D | 119 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | QVQLVESGGGLVQAGGSLRLSCAASGIIFGRNAMGWYRQAPGKERELVAGITRRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADPASPAPGDYWGQGTQVTVSS |
| Synthetic nanobody Nb6 | F | 119 | Severe Acute Respiratory Syndrome Coronavirus 2 , Synthetic Construct | QVQLVESGGGLVQAGGSLRLSCAASGIIFGRNAMGWYRQAPGKERELVAGITRRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADPASPAPGDYWGQGTQVTVSS |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2020-10-27 Deposition Author(s): Anand, A.A. , Azumaya, C.M. , Barile-Hill, A.W. , Barsi-Rhyne, B. , Belyy, V. , Billesboelle, C.B. , Boone, M. , Brilot, A.F. , Bulkley, D. , Chio, C.M. , Chio, U.S. , Desphande, I. , Dickinson, S. , Diwanji, D. , Dobzinski, N. , Faust, B.F. , Garcia-Sastre, A. , Gupta, M. , Gupta, S. , Hoppe, N. , Jin, M. , Kratochvil, H.T. , Krogan, N.J. , Leon, K. , Li, F. , Liang, J. , Liu, Y. , Liu, Y. , Manglik, A. , Merz, G.E. , Moss, F. , Nguyen, H.C. , Nock, S. , Ott, M. , Pospiech, T. , Pourmal, S. , Puchades, C. , Qcrg Structural Biology Consortium , Ralston, C.Y. , Rezelj, V. , Rizo, A.N. , Sangwan, S. , Saunders, R.A. , Schaefer, K. , Schoof, M.S. , Simoneau, C.R. , Smith, A.M. , Sun, M. , Swaney, D.L. , Thompson, M.C. , Trenker, R. , Vignuzzi, M. , Walter, P. , White, K.M. , Zha, B.S. , Zhang, K. , Zimanyi, M.