Cryo-EM structure of E. coli FimH lectin domain bound to Fabs 440-2 and 454-3
Silmon de Monerri NC, Che Y, Lees JA, Jasti J, Wu H, Griffor MC, Kodali S, Hawkins JC, Lypowy J, Ponce C, Curley K, Esadze A, Carcamo J, McLellan T, Keeney D, Illenberger A, Matsuka YV, Shanker S, Chorro L, Gribenko AV, Han S, Anderson AS, Donald RGK
PLoS Pathog (2025) 21 pp. e1012325-e1012325 [ Pubmed: 39970181 DOI: doi:10.1371/journal.ppat.1012325 ]
- 440-2 fab light chain (24 kDa, Protein from Mus musculus)
- 440-2 fab heavy chain (24 kDa, Protein from Mus musculus)
- 445-3 fab heavy chain (24 kDa, Protein from Mus musculus)
- 445-3 fab light chain (23 kDa, Protein from Mus musculus)
- Type 1 fimbrin d-mannose specific adhesin fimh, donor strand complemented with fimg peptide 'triple mutant' (32 kDa, Protein from Escherichia coli)
- Fimh-dsg tm in complex with fabs 440-2 and 445-3 (Complex)
- Fimh-dsg tm (Complex from Escherichia coli)
- Fab 445-3 (Complex from Mus musculus)
- Fab 440-2 (Complex from Mus musculus)
SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 8yz6
Q-score: 0.21
Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Kit Tan T, Rijal P, Chen CP, Cheng SH, Lee WH, Chou YC, Townsend AR, Ma C, Huang KA
PLoS Pathog (2024) 20 pp. e1012246-e1012246 [ DOI: doi:10.1371/journal.ppat.1012246 Pubmed: 38857264 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fab heavy chain of jh-8b (12 kDa, Protein from Homo sapiens)
- Sars-cov-2 delta spike in complex with fab of je-5c (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab light chain of jh-8b (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Resolution: 4.28 Å
EM Method: Single-particle
Fitted PDBs: 8hhz
Q-score: 0.207
Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C
Nat Commun (2023) 14 pp. 311-311 [ DOI: doi:10.1038/s41467-023-35949-8 Pubmed: 36658148 ]
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 delta spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Complex of delta spike and iy-2a with two fabs bound to one spike in 3-rbd-up conformation (550 kDa, Complex)
- Iy-2a fab heavy chain (23 kDa, Protein from Homo sapiens)
- Iy-2a fab light chain (23 kDa, Protein from Homo sapiens)
- Iy-2a (Complex from Homo sapiens)
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv264
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7wth
Q-score: 0.378
Wang L, Fu W, Bao L, Jia Z, Zhang Y, Zhou Y, Wu W, Wu J, Zhang Q, Gao Y, Wang K, Wang Q, Qin C, Wang X
Cell Res (2022) 32 pp. 691-694 [ Pubmed: 35672388 DOI: doi:10.1038/s41422-022-00677-z ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of xgv264 (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron variant spike rbd in complex with fab xgv264 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab xgv264 (Complex)
- Sars-cov-2 omicron variant spike rbd (Complex from Homo sapiens)
- Light chain of xgv264 (11 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7wtj
Q-score: 0.446
Wang L, Fu W, Bao L, Jia Z, Zhang Y, Zhou Y, Wu W, Wu J, Zhang Q, Gao Y, Wang K, Wang Q, Qin C, Wang X
Cell Res (2022) 32 pp. 691-694 [ Pubmed: 35672388 DOI: doi:10.1038/s41422-022-00677-z ]
- Sars-cov-2 omicron variant spike rbd (Complex)
- Light chain of xgv286 (11 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron variant spike rbd in complex with fab xgv286 (Complex from Homo sapiens)
- Heavy chain of xgv286 (12 kDa, Protein from Homo sapiens)
- Fab xgv286 (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of the SARS-CoV-2 S S1 doamin in complex with the mouse antibody Fab fragment, HSW-2
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7uzb
Q-score: 0.334
Fan C, Cohen AA, Park M, Hung AF, Keeffe JR, Gnanapragasam PNP, Lee YE, Gao H, Kakutani LM, Wu Z, Kleanthous H, Malecek KE, Williams JC, Bjorkman PJ
Immunity (2022) 55 pp. 2419- [ Pubmed: 36370711 DOI: doi:10.1016/j.immuni.2022.10.019 ]
- Hsw-2 fab heavy chain (24 kDa, Protein from Mus musculus)
- Hsw-2 fab vh and vl domains (Complex from Mus musculus)
- Hsw-2 fab light chain (23 kDa, Protein from Mus musculus)
- Severe acute respiratory syndrome coronavirus 2 spike glycoprotein s1 domain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hsw-2 fab ch1 and cl domains (Complex from Mus musculus)
- Sars-cov-2 s 6p in complex with hsw-2 fab (25 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv265
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7wee
Q-score: 0.415
Wang K, Jia Z, Bao L, Wang L, Cao L, Chi H, Hu Y, Li Q, Zhou Y, Jiang Y, Zhu Q, Deng Y, Liu P, Wang N, Wang L, Liu M, Li Y, Zhu B, Fan K, Fu W, Yang P, Pei X, Cui Z, Qin L, Ge P, Wu J, Liu S, Chen Y, Huang W, Wang Q, Qin CF, Wang Y, Qin C, Wang X
Nature (2022) 603 pp. 919-925 [ Pubmed: 35090164 DOI: doi:10.1038/s41586-022-04466-x ]
- Fab 265 (Complex)
- The light chain of fab xgv265 (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron mutation spike protein in complex with fab 265 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron mutation spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- The heavy chain of fab xgv265 (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv282
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 7wlc
Q-score: 0.347
Wang K, Jia Z, Bao L, Wang L, Cao L, Chi H, Hu Y, Li Q, Zhou Y, Jiang Y, Zhu Q, Deng Y, Liu P, Wang N, Wang L, Liu M, Li Y, Zhu B, Fan K, Fu W, Yang P, Pei X, Cui Z, Qin L, Ge P, Wu J, Liu S, Chen Y, Huang W, Wang Q, Qin CF, Wang Y, Qin C, Wang X
Nature (2022) 603 pp. 919-925 [ Pubmed: 35090164 DOI: doi:10.1038/s41586-022-04466-x ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron mutation spike protein (Complex from Homo sapiens)
- Fab 265 (Complex)
- Light chain of xgv282 (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron mutation spike protein in complex with fab 265 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of xgv282 (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 Env
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7n28
Q-score: 0.385
Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria-Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F
Adv Sci (2022) 9 pp. e2200063-e2200063 [ DOI: doi:10.1002/advs.202200063 Pubmed: 35319830 ]
- Phosphate ion (94 Da, Ligand)
- J033 antibody heavy chain (24 kDa, Protein from Macaca mulatta)
- 3bnc117 antibody heavy chain (24 kDa, Protein from Homo sapiens)
- Alpha-d-mannopyranose (180 Da, Ligand)
- A complex of hiv-1 env with antibodies 3bnc117 and j033 (Complex from Homo sapiens)
- J033 antibody light chain (23 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp41 (19 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 3bnc117 antibody light chain (23 kDa, Protein from Homo sapiens)
SARS-CoV-2 Spike in complex with Fab of m31A7
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7wuh
Q-score: 0.245
Huang HY, Liao HY, Chen X, Wang SW, Cheng CW, Shahed-Al-Mahmud M, Liu YM, Mohapatra A, Chen TH, Lo JM, Wu YM, Ma HH, Chang YH, Tsai HY, Chou YC, Hsueh YP, Tsai CY, Huang PY, Chang SY, Chao TL, Kao HC, Tsai YM, Chen YH, Wu CY, Jan JT, Cheng TR, Lin KI, Ma C, Wong CH
Sci Transl Med (2022) 14 pp. eabm0899-eabm0899 [ Pubmed: 35230146 DOI: doi:10.1126/scitranslmed.abm0899 ]
- Sars-cov2 spike (Complex from Homo sapiens)
- M31a7 fab heavy chain (25 kDa, Protein from Homo sapiens)
- M31a7 (Complex)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- M31a7 fab light chain (26 kDa, Protein from Homo sapiens)
- Sars-cov2 spike in complex with m31a7 (560 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)