Cryo-EM structure of synthetic tetrameric building block sC4
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8gel
Q-score: 0.439
Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D
Nature (2024) 627 pp. 898-904 [ Pubmed: 38480887 DOI: doi:10.1038/s41586-024-07188-4 ]
- Sc4 (57 kDa, Protein from synthetic construct)
- De novo designed tetramer sc4 (Complex from synthetic construct)
CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 8feg
Q-score: 0.471
Muratspahic E, Deibler K, Han J, Tomasevic N, Jadhav KB, Olive-Marti AL, Hochrainer N, Hellinger R, Koehbach J, Fay JF, Rahman MH, Hegazy L, Craven TW, Varga BR, Bhardwaj G, Appourchaux K, Majumdar S, Muttenthaler M, Hosseinzadeh P, Craik DJ, Spetea M, Che T, Baker D, Gruber CW
Nat Commun (2023) 14 pp. 8064- [ DOI: doi:10.1016/0006-2952(73)90196-2 Pubmed: 38052802 ]
- Kappa-type opioid receptor (34 kDa, Protein from Homo sapiens)
- Ace-tyr-ala-dty-thr-thr-cys-thr-dpn-xt9 (1 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Kappa opioid receptor in complex with gi1 heterotrimer and a peptide ligand (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Scfv16 antibody fragment (26 kDa, Protein from Mus musculus)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Integrin alpha-v beta-8 in complex with minibinder B8_BP_dsulf
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8tcf
Q-score: 0.493
Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zuniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D
Nat Commun (2023) 14 pp. 5660-5660 [ DOI: doi:10.1038/s41467-023-41272-z Pubmed: 37704610 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ternary complex of integrin heterodimer (alpha-v beta-8) and the de novo minibinder protein b8_bp_dslf (Complex from Homo sapiens)
- Minibinder b8_bp_dslf (8 kDa, Protein from synthetic construct)
- Calcium ion (40 Da, Ligand)
- Integrin alpha-v heavy chain (48 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Integrin beta-8 (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8sk7
Q-score: 0.528
Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, Wang J, Venkatesh P, Sappington I, Torres SV, Lauko A, De Bortoli V, Mathieu E, Ovchinnikov S, Barzilay R, Jaakkola TS, DiMaio F, Baek M, Baker D
Nature (2023) 620 pp. 1089-1100 [ Pubmed: 37433327 DOI: doi:10.1038/s41586-023-06415-8 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hemagglutinin (26 kDa, Protein from Influenza A virus)
- Influenza ha (iowa43) bound to rfdiffusion designed minibinder, ha_20 (Complex from Influenza A virus)
- Hemagglutinin ha1 chain (35 kDa, Protein from Influenza A virus)
- Ha_20 minibinder (rfdiffusion-designed) (7 kDa, Protein from unidentified)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7o43
Q-score: 0.425
Mace K, Vadakkepat AK, Redzej A, Lukoyanova N, Oomen C, Braun N, Ukleja M, Lu F, Costa TRD, Orlova EV, Baker D, Cong Q, Waksman G
Nature (2022) 607 pp. 191-196 [ DOI: doi:10.1038/s41586-022-04859-y Pubmed: 35732732 ]
- Hexamer complex of apo-trwk/virb4 with hcp1 (Complex from Escherichia coli)
- Trwk protein (94 kDa, Protein from Escherichia coli)
BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component A)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7l7t
Q-score: 0.428
Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Pena AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB
Nat Commun (2021) 12 pp. 4817-4817 [ Pubmed: 34376662 DOI: doi:10.1038/s41467-021-25087-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosip.v5.2(7s) - gp41 (16 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip reconstructed from a designed nanoparticle, bg505 sosip-t33-31 (component a) (Complex from Human immunodeficiency virus 1)
- Bg505 sosip.v5.2(7s) - gp120 (56 kDa, Protein from Human immunodeficiency virus 1)
BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7l7u
Q-score: 0.439
Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Pena AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB
Nat Commun (2021) 12 pp. 4817-4817 [ Pubmed: 34376662 DOI: doi:10.1038/s41467-021-25087-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosip.v5.2(7s) - gp41 (16 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip reconstructed from a designed nanoparticle, bg505 sosip-t33-31 (component b) (Complex from Human immunodeficiency virus 1)
- Bg505 sosip.v5.2(7s) - gp120 (56 kDa, Protein from Human immunodeficiency virus 1)
BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.33104 (Wk26 time point)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7l8a
Q-score: 0.524
Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Pena AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB
Nat Commun (2021) 12 pp. 4817-4817 [ Pubmed: 34376662 DOI: doi:10.1038/s41467-021-25087-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosip md39 - gp41 (16 kDa, Protein from Human immunodeficiency virus 1)
- Rh.33104 pabc-1 - light chain (8 kDa, Protein from Macaca mulatta)
- Rh.33104 pabc-1 - heavy chain (9 kDa, Protein from Macaca mulatta)
- Bg505 sosip md39 - gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip md39 in complex with the polyclonal fab pabc-1 from animal rh.33104 (wk26 time point) (Complex from Human immunodeficiency virus 1)
BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.33104 (Wk26 time point)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7l8b
Q-score: 0.466
Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Pena AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB
Nat Commun (2021) 12 pp. 4817-4817 [ Pubmed: 34376662 DOI: doi:10.1038/s41467-021-25087-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosip md39 - gp41 (16 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip md39 - gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 sosip md39 in complex with the polyclonal fab pabc-2 from animal rh.33104 (wk26 time point) (Complex from Human immunodeficiency virus 1)
- Rh.33104 pabc-2 - heavy chain (10 kDa, Protein from Macaca mulatta)
- Rh.33104 pabc-2 - light chain (9 kDa, Protein from Macaca mulatta)
BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7l8c
Q-score: 0.513
Antanasijevic A, Sewall LM, Cottrell CA, Carnathan DG, Jimenez LE, Ngo JT, Silverman JB, Groschel B, Georgeson E, Bhiman J, Bastidas R, LaBranche C, Allen JD, Copps J, Perrett HR, Rantalainen K, Cannac F, Yang YR, de la Pena AT, Rocha RF, Berndsen ZT, Baker D, King NP, Sanders RW, Moore JP, Crotty S, Crispin M, Montefiori DC, Burton DR, Schief WR, Silvestri G, Ward AB
Nat Commun (2021) 12 pp. 4817-4817 [ Pubmed: 34376662 DOI: doi:10.1038/s41467-021-25087-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 sosip md39 - gp41 (16 kDa, Protein from Human immunodeficiency virus 1)
- Rh.33104 pabc-3 - light chain (9 kDa, Protein from Macaca mulatta)
- Bg505 sosip md39 in complex with the polyclonal fab pabc-3 from animal rh.33104 (wk26 time point) (Complex from Human immunodeficiency virus 1)
- Rh.33104 pabc-3 - heavy chain (9 kDa, Protein from Macaca mulatta)
- Bg505 sosip md39 - gp120 (52 kDa, Protein from Human immunodeficiency virus 1)