Cryo-EM structure of llama J3 VHH antibody in complex with HIV-1 Env BG505 DS-SOSIP.664
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 7lpn
Q-score: 0.465
Zhou T, Chen L, Gorman J, Wang S, Kwon YD, Lin BC, Louder MK, Rawi R, Stancofski ED, Yang Y, Zhang B, Quigley AF, McCoy LE, Rutten L, Verrips T, Weiss RA, Doria-Rose NA, Shapiro L, Kwong PD
Structure (2022) 30 pp. 862-875.e4 [ Pubmed: 35413243 DOI: doi:10.1016/j.str.2022.03.012 ]
- Hiv-1 env with llama j3 vhh (Complex from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- J3 vhh (14 kDa, Protein from Lama glama)
- Hiv-1 envelope glycoprotein bg505 sosip.664 gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp160 (53 kDa, Protein from Human immunodeficiency virus 1)
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation)
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 7nt9
Q-score: 0.458
Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjaer S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P
Sci Adv (2021) 7 [ Pubmed: 33888467 DOI: doi:10.1126/sciadv.abg7607 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ectodomain of spike glycoprotein from sars-cov-2 expressed in hek cells and purified. data were collected in the presence of excess biliverdin. (426 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7nta
Q-score: 0.436
Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjaer S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P
Sci Adv (2021) 7 [ Pubmed: 33888467 DOI: doi:10.1126/sciadv.abg7607 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ectodomain of s1 protein from sars-cov-2 expressed in hek cells and purified. sample in the presence of excess biliverdin. (426 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Water (18 Da, Ligand)
Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ntc
Q-score: 0.391
Rosa A, Pye VE, Graham C, Muir L, Seow J, Ng KW, Cook NJ, Rees-Spear C, Parker E, Dos Santos MS, Rosadas C, Susana A, Rhys H, Nans A, Masino L, Roustan C, Christodoulou E, Ulferts R, Wrobel AG, Short CE, Fertleman M, Sanders RW, Heaney J, Spyer M, Kjaer S, Riddell A, Malim MH, Beale R, MacRae JI, Taylor GP, Nastouli E, van Gils MJ, Rosenthal PB, Pizzato M, McClure MO, Tedder RS, Kassiotis G, McCoy LE, Doores KJ, Cherepanov P
Sci Adv (2021) 7 [ Pubmed: 33888467 DOI: doi:10.1126/sciadv.abg7607 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- P008_056 fab (Complex from Homo sapiens)
- Stabilised sars-cov-2 spike ectodomain trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Stabilised sars-cov-2 spike ectodomain trimer bound to one p008_056 fab (478 kDa, Complex)
- P008_056 fab heavy chain (27 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- P008_056 fab light chain (25 kDa, Protein from Homo sapiens)
BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 6vo0
Q-score: 0.435
Nogal B, McCoy LE, van Gils MJ, Cottrell CA, Voss JE, Andrabi R, Pauthner M, Liang CH, Messmer T, Nedellec R, Shin M, Turner HL, Ozorowski G, Sanders RW, Burton DR, Ward AB
Sci Adv (2020) 6 pp. eaba0512-eaba0512 [ Pubmed: 32548265 DOI: doi:10.1126/sciadv.aba0512 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab 43a2 (Complex from Oryctolagus cuniculus)
- Bg505 sosip.v5.2 in complex with rabbit fab 43a2 (Complex)
- 43a2 light chain (12 kDa, Protein from Oryctolagus cuniculus)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- 43a2 heavy chain (13 kDa, Protein from Oryctolagus cuniculus)
- Bg505 sosip.v5.2 (Complex from Human immunodeficiency virus 1)
HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
Resolution: 3.86 Å
EM Method: Single-particle
Fitted PDBs: 6u59
Q-score: 0.393
Yang YR, McCoy LE, van Gils MJ, Andrabi R, Turner HL, Yuan M, Cottrell CA, Ozorowski G, Voss J, Pauthner M, Polveroni TM, Messmer T, Wilson IA, Sanders RW, Burton DR, Ward AB
J Virol (2020) 94 [ DOI: doi:10.1128/JVI.01861-19 Pubmed: 31941772 ]
- Hiv-1 b41 sosip.664 in complex with rabbit antibody 13b (570 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Rabbit antibody 13b (Complex from Oryctolagus cuniculus)
- Rabbit antibody 13b fragment antigen binding light chain (11 kDa, Protein from Oryctolagus cuniculus)
- Rabbit antibody 13b fragment antigen binding heavy chain (12 kDa, Protein from Oryctolagus cuniculus)
- Sosip.664 gp120,sosip.664 gp120 (58 kDa, Protein from Human immunodeficiency virus 1)
- Sosip.664 gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 b41 sosip.664 (Complex from Human immunodeficiency virus 1)
HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Resolution: 4.71 Å
EM Method: Single-particle
Fitted PDBs: 6did
Q-score: 0.23
Bianchi M, Turner HL, Nogal B, Cottrell CA, Oyen D, Pauthner M, Bastidas R, Nedellec R, McCoy LE, Wilson IA, Burton DR, Ward AB, Hangartner L
Immunity (2018) 49 pp. 288-300.e8 [ Pubmed: 30097292 DOI: doi:10.1016/j.immuni.2018.07.009 ]
- Envelope glycoprotein gp160 (54 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp160 (17 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hiv env bg505 sosip with polyclonal fabs from immunized rabbit #3417 post-boost#1 (Complex from Homo sapiens)
- Monoclonal antibody 10a heavy chain (22 kDa, Protein from Oryctolagus cuniculus)
- Monoclonal antibody 10a light chain (23 kDa, Protein from Oryctolagus cuniculus)
Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6crq
Q-score: 0.363
Schiffner T, Pallesen J, Russell RA, Dodd J, de Val N, LaBranche CC, Montefiori D, Tomaras GD, Shen X, Harris SL, Moghaddam AE, Kalyuzhniy O, Sanders RW, McCoy LE, Moore JP, Ward AB, Sattentau QJ
PLoS Pathog (2018) 14 pp. e1006986-e1006986 [ DOI: doi:10.1371/journal.ppat.1006986 Pubmed: 29746590 ]
- Envelope glycoprotein gp160 (53 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp160 (17 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Glutaraldehyde-treated bg505 sosip.664 env in complex with pgv04 fab (550 kDa, Complex from Human immunodeficiency virus 1)
- Pgv04 vl (23 kDa, Protein from Homo sapiens)
- Pgv04 vh (24 kDa, Protein from Homo sapiens)