Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
Resolution: 4.03 Å
EM Method: Single-particle
Fitted PDBs: 8to9
Q-score: 0.305
Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD
Cell (2024) 187 pp. 7214-7231.e23 [ Pubmed: 39471811 DOI: doi:10.1016/j.cell.2024.10.003 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Trnm-f*01 light chain (11 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp120 (52 kDa, Protein from Homo sapiens)
- Trnm-f*01 heavy chain (13 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp41 (17 kDa, Protein from Homo sapiens)
- Trnm-f*01 fab in complex with hiv-1 env trimer conc sosip (Complex from Macaca mulatta)
Cryo-EM structure of the HIV-1 JR-FL IDL Env trimer in complex with PGT122 Fab
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 9ber
Q-score: 0.327
Zhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang GY, Geng H, Lai YT, Zhou T, Mascola JR, Mothes W, Kwong PD, Lusso P
Cell Rep (2024) 43 pp. 114518-114518 [ Pubmed: 39028623 DOI: doi:10.1016/j.celrep.2024.114518 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pgt122 heavy chain (14 kDa, Protein from Homo sapiens)
- Sulfate ion (96 Da, Ligand)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Pgt122 light chain (11 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Cryo-em structure of the hiv-1 jr-fl idl env trimer in complex with pgt122 fab (Complex from Human immunodeficiency virus 1)
Cryo-EM structure of the HIV-1 WITO IDL Env trimer in complex with PGT122 Fab
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 9bf6
Q-score: 0.241
Zhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang GY, Geng H, Lai YT, Zhou T, Mascola JR, Mothes W, Kwong PD, Lusso P
Cell Rep (2024) 43 pp. 114518-114518 [ Pubmed: 39028623 DOI: doi:10.1016/j.celrep.2024.114518 ]
- Phosphate ion (94 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pgt122 heavy chain (14 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Cryo-em structure of the hiv-1 wito idl env trimer in complex with pgt122 fab (Complex from Human immunodeficiency virus 1)
- Pgt122 light chain (11 kDa, Protein from Homo sapiens)
Human pseudouridine synthase 3 (PUS3 R116A mutant)
Lin TY, Kleemann L, Jezowski J, Dobosz D, Rawski M, Indyka P, Wazny G, Mehta R, Chramiec-Glabik A, Koziej L, Ranff T, Fufezan C, Wawro M, Kochan J, Bereta J, Leidel SA, Glatt S
Mol Cell (2024) 84 pp. 2472-2489.e8 [ DOI: doi:10.1016/j.molcel.2024.06.013 Pubmed: 38996458 ]
- Pseudouridine synthase 3 homodimer (Protein from Homo sapiens)
- Homodimer of human pus3 (r116a mutant) (110 kDa, Complex from Homo sapiens)
Human pseudouridine synthase 3 (wild type)
Lin TY, Kleemann L, Jezowski J, Dobosz D, Rawski M, Indyka P, Wazny G, Mehta R, Chramiec-Glabik A, Koziej L, Ranff T, Fufezan C, Wawro M, Kochan J, Bereta J, Leidel SA, Glatt S
Mol Cell (2024) 84 pp. 2472-2489.e8 [ DOI: doi:10.1016/j.molcel.2024.06.013 Pubmed: 38996458 ]
- Pseudouridine synthase 3 homodimer (Protein from Homo sapiens)
- Homodimer of human pus3 (wild type) (110 kDa, Complex from Homo sapiens)
Structure of E6AP-E6 complex in Det1 state
Resolution: 4.15 Å
EM Method: Single-particle
Fitted PDBs: 8jrq
Q-score: 0.186
Wang Z, Fan F, Li Z, Ye F, Wang Q, Gao R, Qiu J, Lv Y, Lin M, Xu W, Luo C, Yu X
Nat Commun (2024) 15 pp. 3531-3531 [ DOI: doi:10.1038/s41467-024-47586-w Pubmed: 38670961 ]
- Ubiquitin-protein ligase e3a (100 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E6ap-e6 complex (Complex from Homo sapiens)
- Protein e6 (19 kDa, Protein from Human papillomavirus 16)
Structure of E6AP-E6 complex in Det2 state
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8jrr
Q-score: 0.164
Wang Z, Fan F, Li Z, Ye F, Wang Q, Gao R, Qiu J, Lv Y, Lin M, Xu W, Luo C, Yu X
Nat Commun (2024) 15 pp. 3531-3531 [ DOI: doi:10.1038/s41467-024-47586-w Pubmed: 38670961 ]
- Protein e6 (16 kDa, Protein from Human papillomavirus 16)
- E6ap-e6 complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-protein ligase e3a (100 kDa, Protein from Homo sapiens)
10E8-GT10.2 immunogen in complex with human Fab 10E8 and mouse Fab W6-10
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8sx3
Q-score: 0.378
Schiffner T, Phung I, Ray R, Irimia A, Tian M, Swanson O, Lee JH, Lee CD, Marina-Zarate E, Cho SY, Huang J, Ozorowski G, Skog PD, Serra AM, Rantalainen K, Allen JD, Baboo S, Rodriguez OL, Himansu S, Zhou J, Hurtado J, Flynn CT, McKenney K, Havenar-Daughton C, Saha S, Shields K, Schulze S, Smith ML, Liang CH, Toy L, Pecetta S, Lin YC, Willis JR, Sesterhenn F, Kulp DW, Hu X, Cottrell CA, Zhou X, Ruiz J, Wang X, Nair U, Kirsch KH, Cheng HL, Davis J, Kalyuzhniy O, Liguori A, Diedrich JK, Ngo JT, Lewis V, Phelps N, Tingle RD, Spencer S, Georgeson E, Adachi Y, Kubitz M, Eskandarzadeh S, Elsliger MA, Amara RR, Landais E, Briney B, Burton DR, Carnathan DG, Silvestri G, Watson CT, Yates 3rd JR, Paulson JC, Crispin M, Grigoryan G, Ward AB, Sok D, Alt FW, Wilson IA, Batista FD, Crotty S, Schief WR
Nat Immunol (2024) 25 pp. 1073-1082 [ Pubmed: 38816615 DOI: doi:10.1038/s41590-024-01833-w ]
- 10e8-gt10.2 immunogen (Complex from synthetic construct)
- 10e8-gt10.2 immunogen (21 kDa, Protein from synthetic construct)
- 10e8 fab heavy chain, 10e8 light chain (Complex from Homo sapiens)
- 10e8-gt10.2 immunogen in complex with human fab 10e8 and mouse fab w6-10 (Complex)
- W6-10 mouse fab heavy chain, w6-10 mouse light chain (Complex from Mus musculus)
- 10e8 light chain (22 kDa, Protein from Homo sapiens)
- W6-10 mouse fab heavy chain (23 kDa, Protein from Mus musculus)
- 10e8 fab heavy chain (25 kDa, Protein from Homo sapiens)
- W6-10 mouse light chain (23 kDa, Protein from Mus musculus)
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)
Resolution: 4.71 Å
EM Method: Single-particle
Fitted PDBs: 8zbz
Q-score: 0.272
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with 3 d1f6 fabs (1 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 8zc0
Q-score: 0.338
Liu B, Niu X, Deng Y, Zhang Z, Wang Y, Gao X, Liang H, Li Z, Wang Q, Cheng Y, Chen Q, Huang S, Pan Y, Su M, Lin X, Niu C, Chen Y, Yang W, Zhang Y, Yan Q, He J, Zhao J, Chen L, Xiong X
Cell Rep (2024) 43 pp. 114265-114265 [ DOI: doi:10.1016/j.celrep.2024.114265 Pubmed: 38805396 ]
- Sars-cov-2 omicron ba.2 spike trimer (6p) in complex with 3 d1f6 fabs (2 rbd up) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (137 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of d1f6 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of d1f6 fab (24 kDa, Protein from Homo sapiens)