Cryo-EM structure of Antibody 12-16 in complex with prefusion SARS-CoV-2 Spike glycoprotein
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7ukl
Q-score: 0.49
Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JF, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VK, Chan CC, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD
Immunity (2023) 56 pp. 2442- [ DOI: doi:10.1016/j.immuni.2023.09.003 Pubmed: 37776849 ]
- 12-16 fab light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Antibody 12-16 in complex with prefusion sars-cov-2 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 12-16 fab heavy chain (14 kDa, Protein from Homo sapiens)
Cryo-EM local refinement of antibody SKV09 in complex with VEEV alphavirus spike glycoprotein
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 8deq
Q-score: 0.19
Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG, Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M, Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schon A, Schramm CA, Shen CH, Shi W, Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong PD, Roederer M
Cell (2023) 186 pp. 2672-2689.e25 [ Pubmed: 37295404 DOI: doi:10.1016/j.cell.2023.05.019 ]
- Cryo-em local refinement of antibody skv09 in complex with veev alphavirus spike glycoprotein (Complex from Venezuelan equine encephalitis virus)
- Skv09 fab heavy chain (13 kDa, Protein from Macaca)
- Spike glycoprotein e1 (43 kDa, Protein from Venezuelan equine encephalitis virus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Skv09 fab light chain (11 kDa, Protein from Macaca)
SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7vgr
Q-score: 0.504
Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T
Nat Commun (2022) 13 pp. 4399-4399 [ DOI: doi:10.1038/s41467-022-32019-3 Pubmed: 35931673 ]
- Membrane protein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yn7756_1 fab heavy chain (25 kDa, Protein from Mus musculus)
- Membrane protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Yn7756_1 fab (Complex from Mus musculus)
- Yn7756_1 fab light chain (24 kDa, Protein from Mus musculus)
- Sars-cov-2 m protein dimer (long form) in complex with yn7756_1 fab (Complex)
SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vgs
Q-score: 0.451
Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T
Nat Commun (2022) 13 pp. 4399-4399 [ DOI: doi:10.1038/s41467-022-32019-3 Pubmed: 35931673 ]
- Yn7717_9 fab heavy chain (24 kDa, Protein from Mus musculus)
- Membrane protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 m protein dimer (short form) in complex with yn7717_9 fab (Complex)
- Membrane protein (28 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yn7717_9 fab light chain (23 kDa, Protein from Mus musculus)
- Yn7717_9 fab (Complex from Mus musculus)
human NTCP in complex with YN69083 Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7fci
Q-score: 0.497
Park JH, Iwamoto M, Yun JH, Uchikubo-Kamo T, Son D, Jin Z, Yoshida H, Ohki M, Ishimoto N, Mizutani K, Oshima M, Muramatsu M, Wakita T, Shirouzu M, Liu K, Uemura T, Nomura N, Iwata S, Watashi K, Tame JRH, Nishizawa T, Lee W, Park SY
Nature (2022) 606 pp. 1027-1031 [ DOI: doi:10.1038/s41586-022-04857-0 Pubmed: 35580630 ]
- Fab light chain (23 kDa, Protein from Mus musculus)
- Ntcp (Complex from Homo sapiens)
- Fab light chain,fab heavy chain (Complex from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Human ntcp in complex with yn69083 (89 kDa, Cellular component)
- Fab heavy chain (27 kDa, Protein from Mus musculus)
Cryo-EM structure of human NTCP complexed with YN69202Fab
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7vad
Q-score: 0.399
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
- Fab (Complex)
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Ntcp: (Complex from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Complex of ntcp and fab (Complex from Homo sapiens)
Cryo-EM structure of Rat NTCP complexed with YN69202Fab
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7vaf
Q-score: 0.461
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Fab (Complex from Rattus norvegicus)
- Complex of ntcp and fab (Complex from Mus musculus)
- Ntcp (Complex)
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Rattus norvegicus)
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 7vag
Q-score: 0.401
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Fab (Complex)
- Ntcp (Complex from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Complex of ntcp and fab in the presence of myristoylated pres1 peptide (Complex from Homo sapiens)
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
Cryo-EM structure of human NTCP (wild-type) complexed with YN69202Fab
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 7wsi
Q-score: 0.434
Asami J, Kimura KT, Fujita-Fujiharu Y, Ishida H, Zhang Z, Nomura Y, Liu K, Uemura T, Sato Y, Ono M, Yamamoto M, Noda T, Shigematsu H, Drew D, Iwata S, Shimizu T, Nomura N, Ohto U
Nature (2022) 606 pp. 1021-1026 [ DOI: doi:10.1038/s41586-022-04845-4 Pubmed: 35580629 ]
- Fab heavy chain from antibody igg clone number yn69202 (26 kDa, Protein from Mus musculus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab (Complex)
- Ntcp (Complex from Homo sapiens)
- Complex of ntcp and fab (Complex from Homo sapiens)
- Fab light chain from antibody igg clone number yn69202 (24 kDa, Protein from Mus musculus)
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 7ls9
Q-score: 0.429
Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L, Huang Y, Ho DD, Kwong PD, Sheng Z, Shapiro L
Structure (2021) 29 pp. 655-663.e4 [ DOI: doi:10.1016/j.str.2021.05.014 Pubmed: 34111408 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1-57 fab light chain (23 kDa, Protein from Homo sapiens)
- Prefusion sars-cov-2 spike glycoprotein in complex with 1-57 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 1-57 fab heavy chain (26 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)