Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
Reveiz M, Xu K, Lee M, Wang S, Olia AS, Harris DR, Liu K, Liu T, Schaub AJ, Stephens T, Wang Y, Zhang B, Huang R, Tsybovsky Y, Kwong PD, Rawi R
Front Immunol (2024) 15 pp. 1484029-1484029 [ Pubmed: 39611147 DOI: doi:10.3389/fimmu.2024.1484029 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 env trimer complexed with antibody fab (Complex from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Antibody acs202 fab light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Antibody acs202 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Antibody fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8we4
Q-score: 0.462
Li W, Xu Z, Niu T, Xie Y, Zhao Z, Li D, He Q, Sun W, Shi K, Guo W, Chang Z, Liu K, Fan Z, Qi J, Gao GF
EMBO J (2024) 43 pp. 1484-1498 [ Pubmed: 38467833 DOI: doi:10.1038/s44318-024-00062-z ]
- Ace2 (Complex from Homo sapiens)
- Sars-cov-2 omicron xbb.1.5 rbd complexed with human ace2 and fab s304 (Complex)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fabs304 (Complex from Homo sapiens)
- S304 fab heavy chain (24 kDa, Protein from Homo sapiens)
- S304 fab light chain (23 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 omicron xbb.1.5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (92 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8hrx
Q-score: 0.523
Asami J, Park JH, Nomura Y, Kobayashi C, Mifune J, Ishimoto N, Uemura T, Liu K, Sato Y, Zhang Z, Muramatsu M, Wakita T, Drew D, Iwata S, Shimizu T, Watashi K, Park SY, Nomura N, Ohto U
Nat Struct Mol Biol (2024) 31 pp. 447-454 [ Pubmed: 38233573 DOI: doi:10.1038/s41594-023-01191-5 ]
- Ntcp-myr-pres1-yn9048fab (Complex from Homo sapiens)
- Pres1 protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Fab heavy chain from antibody igg clone number yn9048 (26 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab light chain from antibody igg clone number yn9048 (23 kDa, Protein from Ondatra zibethicus)
Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 8hry
Q-score: 0.523
Asami J, Park JH, Nomura Y, Kobayashi C, Mifune J, Ishimoto N, Uemura T, Liu K, Sato Y, Zhang Z, Muramatsu M, Wakita T, Drew D, Iwata S, Shimizu T, Watashi K, Park SY, Nomura N, Ohto U
Nat Struct Mol Biol (2024) 31 pp. 447-454 [ Pubmed: 38233573 DOI: doi:10.1038/s41594-023-01191-5 ]
- Fab light chain from antibody igg clone number yn9016 (23 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab heavy chain from antibody igg clone number yn9016 (25 kDa, Protein from Ondatra zibethicus)
- Large s protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Ntcp-myr-pres1-yn9016fab (Complex from Homo sapiens)
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)