Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 9bio
Q-score: 0.547
Cale EM, Shen CH, Olia AS, Radakovich NA, Rawi R, Yang Y, Ambrozak DR, Bennici AK, Chuang GY, Crooks ED, Driscoll JI, Lin BC, Louder MK, Madden PJ, Messina MA, Osawa K, Stewart-Jones GBE, Verardi R, Vrakas Z, Xie D, Zhang B, Binley JM, Connors M, Koup RA, Pierson TC, Doria-Rose NA, Kwong PD, Mascola JR, Gorman J
Cell Rep (2024) 43 pp. 115010-115010 [ Pubmed: 39675002 DOI: doi:10.1016/j.celrep.2024.115010 ]
- 3bnc117 heavy chain (24 kDa, Protein from Homo sapiens)
- Vrc44 and 3bnc117 fabs with repaired c1080 env trimer (Complex from Human immunodeficiency virus 1)
- Phosphate ion (94 Da, Ligand)
- Envelope glycoprotein gp160 (54 kDa, Protein from Human immunodeficiency virus 1)
- Vrc44.01 light chain (11 kDa, Protein from Homo sapiens)
- 3bnc117 light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp41 (19 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Vrc44.01 heavy chain (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
Reveiz M, Xu K, Lee M, Wang S, Olia AS, Harris DR, Liu K, Liu T, Schaub AJ, Stephens T, Wang Y, Zhang B, Huang R, Tsybovsky Y, Kwong PD, Rawi R
Front Immunol (2024) 15 pp. 1484029-1484029 [ Pubmed: 39611147 DOI: doi:10.3389/fimmu.2024.1484029 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 env trimer complexed with antibody fab (Complex from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Antibody acs202 fab light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Antibody acs202 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Antibody fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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 ]
- 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)
- 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)
- Pgt122 heavy chain (14 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
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)
- Cryo-em structure of the hiv-1 wito idl env trimer in complex with pgt122 fab (Complex from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Pgt122 light chain (11 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Pgt122 heavy chain (14 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8pg0
Q-score: 0.528
Ciuta AD, Nosol K, Kowal J, Mukherjee S, Ramirez AS, Stieger B, Kossiakoff AA, Locher KP
Nat Commun (2023) 14 pp. 5774-5774 [ DOI: doi:10.1038/s41467-023-41552-8 Pubmed: 37723174 ]
- Bicarbonate ion (61 Da, Ligand)
- Solute carrier organic anion transporter family member 1b3 (77 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Fab19 (light chain, variable region) (23 kDa, Protein from Homo sapiens)
- Human oatp1b3 (180 kDa, Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab19 (heavy chain, variable region) (25 kDa, Protein from Homo sapiens)
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8euv
Q-score: 0.586
Banach BB, Pletnev S, Olia AS, Xu K, Zhang B, Rawi R, Bylund T, Doria-Rose NA, Nguyen TD, Fahad AS, Lee M, Lin BC, Liu T, Louder MK, Madan B, McKee K, O'Dell S, Sastry M, Schon A, Bui N, Shen CH, Wolfe JR, Chuang GY, Mascola JR, Kwong PD, DeKosky BJ
Nat Commun (2023) 14 pp. 7593-7593 [ Pubmed: 37989731 DOI: doi:10.1038/s41467-023-42098-5 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 ds-sosip vrc34.01-combo1 fab complex (Complex from Human immunodeficiency virus 1)
- Vrc34.01-combo1 fab variable light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Vrc34.01-combo1 fab variable heavy chain (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8euw
Q-score: 0.553
Banach BB, Pletnev S, Olia AS, Xu K, Zhang B, Rawi R, Bylund T, Doria-Rose NA, Nguyen TD, Fahad AS, Lee M, Lin BC, Liu T, Louder MK, Madan B, McKee K, O'Dell S, Sastry M, Schon A, Bui N, Shen CH, Wolfe JR, Chuang GY, Mascola JR, Kwong PD, DeKosky BJ
Nat Commun (2023) 14 pp. 7593-7593 [ Pubmed: 37989731 DOI: doi:10.1038/s41467-023-42098-5 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Vrc34.01-mm28 fab variable heavy chain (23 kDa, Protein from Homo sapiens)
- Vrc34.01-mm28 fab variable light chain (23 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip vrc34.01-mm28 fab complex (Complex from Human immunodeficiency virus 1)
Cryo-EM structure of human ferroportin/slc40 bound to Ca2+ in nanodisc
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8dl6
Q-score: 0.468
Shen J, Wilbon AS, Zhou M, Pan Y
eLife (2023) 12 [ DOI: doi:10.7554/eLife.82947 Pubmed: 36648329 ]
- Cryo-em structure of human ferroportin/slc40 bound to ca2+ in nanodisc (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Solute carrier family 40 member 1 (63 kDa, Protein from Homo sapiens)
- 11f9 heavy-chain (25 kDa, Protein from Mus musculus)
- Calcium ion (40 Da, Ligand)
- 11f9 light-chain (23 kDa, Protein from Mus musculus)
Cryo-EM structure of human ferroportin/slc40 bound to minihepcidin PR73 in nanodisc
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8dl7
Q-score: 0.514
Wilbon AS, Shen J, Ruchala P, Zhou M, Pan Y
PLoS Biol (2023) 21 pp. e3001936-e3001936 [ Pubmed: 36649314 DOI: doi:10.1371/journal.pbio.3001936 ]
- Water (18 Da, Ligand)
- Cryo-em structure of human ferroportin/slc40 bound to minihepcidin pr73 in nanodisc (Complex from Homo sapiens)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Minihepcidin pr73 (1 kDa, Protein from synthetic construct)
- Solute carrier family 40 member 1 (63 kDa, Protein from Homo sapiens)
- 11f9 heavy-chain (25 kDa, Protein from Mus musculus)
- 11f9 light-chain (23 kDa, Protein from Mus musculus)
Cryo-EM structure of human ferroportin/slc40 bound to Co2+ in nanodisc
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8dl8
Q-score: 0.48
Wilbon AS, Shen J, Ruchala P, Zhou M, Pan Y
PLoS Biol (2023) 21 pp. e3001936-e3001936 [ Pubmed: 36649314 DOI: doi:10.1371/journal.pbio.3001936 ]
- Water (18 Da, Ligand)
- Solute carrier family 40 member 1 (63 kDa, Protein from Homo sapiens)
- 11f9 heavy-chain (25 kDa, Protein from Mus musculus)
- Cobalt (ii) ion (58 Da, Ligand)
- Cryo-em structure of human ferroportin/slc40 bound to co2+ in nanodisc (Complex from Homo sapiens)
- 11f9 light-chain (23 kDa, Protein from Mus musculus)