HIV-1 BG505 Env SOSIP in complex with bovine Fab Bess4 and non-human primate Fab RM20A3
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8tq1
Q-score: 0.512
Altman PX, Ozorowski G, Stanfield RL, Haakenson J, Appel M, Parren M, Lee WH, Sang H, Woehl J, Saye-Francisco K, Sewall LM, Joyce C, Song G, Porter K, Landais E, Andrabi R, Wilson IA, Ward AB, Mwangi W, Smider VV, Burton DR, Sok D
PLoS Pathog (2024) 20 pp. e1012042-e1012042 [ DOI: doi:10.1371/journal.ppat.1012042 Pubmed: 39250525 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Nhp rm20a3 fab heavy chain (13 kDa, Protein from Macaca mulatta)
- Bovine bess4 fab heavy chain (17 kDa, Protein from Bos taurus)
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 envelope glycoprotein bg505 sosip.664 gp120 (57 kDa, Protein from Human immunodeficiency virus 1)
- Nhp rm20a3 fab light chain (13 kDa, Protein from Macaca mulatta)
- Hiv-1 bg505 sosip env in complex with bovine bess4 fab and nhp rm20a3 fab (Complex from Human immunodeficiency virus 1)
HIV Env BG505_MD39_B11 SOSIP boosting trimer in complex with B11_d77.7 mouse Fab and RM20A3 Fab
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8f92
Q-score: 0.516
Xie Z, Lin YC, Steichen JM, Ozorowski G, Kratochvil S, Ray R, Torres JL, Liguori A, Kalyuzhniy O, Wang X, Warner JE, Weldon SR, Dale GA, Kirsch KH, Nair U, Baboo S, Georgeson E, Adachi Y, Kubitz M, Jackson AM, Richey ST, Volk RM, Lee JH, Diedrich JK, Prum T, Falcone S, Himansu S, Carfi A, Yates 3rd JR, Paulson JC, Sok D, Ward AB, Schief WR, Batista FD
Science (2024) 384 pp. eadk0582-eadk0582 [ DOI: doi:10.1126/science.adk0582 Pubmed: 38753770 ]
- Bg505_md39_b11 gp120 (54 kDa, Protein from Human immunodeficiency virus)
- Rm20a3 fab light chain (13 kDa, Protein from Macaca mulatta)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hiv-1 env bg505_md39_b11 sosip in complex with fabs b11_d77.7 and rm20a3 (Complex)
- B11_d77.7 fab heavy chain (14 kDa, Protein from Mus musculus)
- B11_d77.7 fab kappa light chain (11 kDa, Protein from Mus musculus)
- Rm20a3 fab heavy chain (13 kDa, Protein from Macaca mulatta)
- Bg505_md39_b11 gp41 (18 kDa, Protein from Human immunodeficiency virus)
HIV Env BG505_MD39_B16 SOSIP boosting trimer in complex with B16_d77.5 mouse Fab and RM20A3 Fab
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vfv
Q-score: 0.495
Xie Z, Lin YC, Steichen JM, Ozorowski G, Kratochvil S, Ray R, Torres JL, Liguori A, Kalyuzhniy O, Wang X, Warner JE, Weldon SR, Dale GA, Kirsch KH, Nair U, Baboo S, Georgeson E, Adachi Y, Kubitz M, Jackson AM, Richey ST, Volk RM, Lee JH, Diedrich JK, Prum T, Falcone S, Himansu S, Carfi A, Yates 3rd JR, Paulson JC, Sok D, Ward AB, Schief WR, Batista FD
Science (2024) 384 pp. eadk0582-eadk0582 [ DOI: doi:10.1126/science.adk0582 Pubmed: 38753770 ]
- Rm20a3 fab light chain (13 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- B16_d77.5 mouse fab light chain fv (12 kDa, Protein from Mus musculus)
- Iv env bg505_md39_b16 sosip boosting trimer in complex with b16_d77.5 mouse fab and rm20a3 fab (Complex from Human immunodeficiency virus 1)
- B16_d77.5 mouse fab heavy chain fv (13 kDa, Protein from Mus musculus)
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Rm20a3 fab heavy chain (13 kDa, Protein from Macaca mulatta)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8t4k
Q-score: 0.62
Steichen JM, Phung I, Salcedo E, Ozorowski G, Willis JR, Baboo S, Liguori A, Cottrell CA, Torres JL, Madden PJ, Ma KM, Sutton HJ, Lee JH, Kalyuzhniy O, Allen JD, Rodriguez OL, Adachi Y, Mullen TM, Georgeson E, Kubitz M, Burns A, Barman S, Mopuri R, Metz A, Altheide TK, Diedrich JK, Saha S, Shields K, Schultze SE, Smith ML, Schiffner T, Burton DR, Watson CT, Bosinger SE, Crispin M, Yates 3rd JR, Paulson JC, Ward AB, Sok D, Crotty S, Schief WR
Science (2024) 384 pp. eadj8321-eadj8321 [ Pubmed: 38753769 DOI: doi:10.1126/science.adj8321 ]
- Md64 n332-gt5 sosip gp41 (18 kDa, Protein from Human immunodeficiency virus 1)
- Md64 n332-gt5 sosip gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Md64 n332-gt5 sosip (Complex from Human immunodeficiency virus 1)
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8dt8
Q-score: 0.443
Misson Mindrebo L, Liu H, Ozorowski G, Tran Q, Woehl J, Khalek I, Smith JM, Barman S, Zhao F, Keating C, Limbo O, Verma M, Liu J, Stanfield RL, Zhu X, Turner HL, Sok D, Huang PS, Burton DR, Ward AB, Wilson IA, Jardine JG
PNAS (2023) 120 pp. e2216612120-e2216612120 [ Pubmed: 37276407 DOI: doi:10.1073/pnas.2216612120 ]
- Lm18 nanobody (14 kDa, Protein from synthetic construct)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Lm18/nb136 bispecific tetra-nanobody immunoglobulin in complex with sars-cov-2-6p-mut7 s protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Nb136 nanobody (13 kDa, Protein from synthetic construct)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 7t2p
Q-score: 0.422
Zhao F, Berndsen ZT, Pedreno-Lopez N, Burns A, Allen JD, Barman S, Lee WH, Chakraborty S, Gnanakaran S, Sewall LM, Ozorowski G, Limbo O, Song G, Yong P, Callaghan S, Coppola J, Weisgrau KL, Lifson JD, Nedellec R, Voigt TB, Laurino F, Louw J, Rosen BC, Ricciardi M, Crispin M, Desrosiers RC, Rakasz EG, Watkins DI, Andrabi R, Ward AB, Burton DR, Sok D
Nat Commun (2022) 13 pp. 5236-5236 [ Pubmed: 36068229 DOI: doi:10.1038/s41467-022-32783-2 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelope glycoprotein gp41 (18 kDa, Protein from Simian immunodeficiency virus)
- K11 fab light chain (25 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp120 (60 kDa, Protein from Simian immunodeficiency virus)
- Sivmac239.k180s sosip trimer in complex with 3 copies of k11 fab (Complex from Simian immunodeficiency virus)
- K11 fab heavy chain (53 kDa, Protein from Macaca mulatta)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7t4g
Q-score: 0.406
Zhao F, Berndsen ZT, Pedreno-Lopez N, Burns A, Allen JD, Barman S, Lee WH, Chakraborty S, Gnanakaran S, Sewall LM, Ozorowski G, Limbo O, Song G, Yong P, Callaghan S, Coppola J, Weisgrau KL, Lifson JD, Nedellec R, Voigt TB, Laurino F, Louw J, Rosen BC, Ricciardi M, Crispin M, Desrosiers RC, Rakasz EG, Watkins DI, Andrabi R, Ward AB, Burton DR, Sok D
Nat Commun (2022) 13 pp. 5236-5236 [ Pubmed: 36068229 DOI: doi:10.1038/s41467-022-32783-2 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- K11 igg heavy chain (53 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp41 (18 kDa, Protein from Simian immunodeficiency virus)
- K11 igg light chain (25 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp120 (60 kDa, Protein from Simian immunodeficiency virus)
- Sivmac239.k180s sosip trimer in complex with 3 copies of k11 igg (Complex from Simian immunodeficiency virus)
AMC009 SOSIPv5.2 in complex with Fabs ACS114 and ACS122
Resolution: 3.99 Å
EM Method: Single-particle
Fitted PDBs: 7zlk
Q-score: 0.362
van Schooten J, Schorcht A, Farokhi E, Umotoy JC, Gao H, van den Kerkhof TLGM, Dorning J, Rijkhold Meesters TG, van der Woude P, Burger JA, Bijl T, Ghalaiyini R, Torrents de la Pena A, Turner HL, Labranche CC, Stanfield RL, Sok D, Schuitemaker H, Montefiori DC, Burton DR, Ozorowski G, Seaman MS, Wilson IA, Sanders RW, Ward AB, van Gils MJ
PLoS Pathog (2022) 18 pp. e1010945-e1010945 [ DOI: doi:10.1371/journal.ppat.1010945 Pubmed: 36395347 ]
- Acs114 light chain (12 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Amc009 sosipv5.2 envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Amc009 sosipv5.2 in complex with fabs acs114 and acs122 (17 MDa, Complex from Human immunodeficiency virus 1)
- Amc009 sosipv5.2 envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Acs122 heavy chain (13 kDa, Protein from Homo sapiens)
- Acs122 light chain (11 kDa, Protein from Homo sapiens)
- Acs114 heavy chain (13 kDa, Protein from Homo sapiens)
SARS-CoV-2-6P-Mut7 S protein (C3 symmetry)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7ru1
Q-score: 0.563
Zhao F, Keating C, Ozorowski G, Shaabani N, Francino-Urdaniz IM, Barman S, Limbo O, Burns A, Zhou P, Ricciardi MJ, Woehl J, Tran Q, Turner HL, Peng L, Huang D, Nemazee D, Andrabi R, Sok D, Teijaro JR, Whitehead TA, Ward AB, Burton DR, Jardine JG
iScience (2022) 25 pp. 104914-104914 [ Pubmed: 35971553 DOI: doi:10.1016/j.isci.2022.104914 ]
SARS-CoV-2-6P-Mut7 S protein (asymmetric)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ru2
Q-score: 0.521
Zhao F, Keating C, Ozorowski G, Shaabani N, Francino-Urdaniz IM, Barman S, Limbo O, Burns A, Zhou P, Ricciardi MJ, Woehl J, Tran Q, Turner HL, Peng L, Huang D, Nemazee D, Andrabi R, Sok D, Teijaro JR, Whitehead TA, Ward AB, Burton DR, Jardine JG
iScience (2022) 25 pp. 104914-104914 [ Pubmed: 35971553 DOI: doi:10.1016/j.isci.2022.104914 ]