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 [ DOI: doi:10.3389/fimmu.2024.1484029 Pubmed: 39611147 ]
- Hiv-1 env trimer complexed with antibody fab (Complex from Human immunodeficiency virus 1)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Antibody acs202 fab light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Antibody acs202 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Antibody fab (Complex from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8f7t
Q-score: 0.351
Olia AS, Cheng C, Zhou T, Biju A, Harris DR, Changela A, Duan H, Ivleva VB, Kong WP, Ou L, Rawi R, Tsybovsky Y, Van Wazer DJ, Corrigan AR, Gonelli CA, Lee M, McKee K, Narpala S, O'Dell S, Parchment DK, Stancofski ED, Stephens T, Tan I, Teng IT, Wang S, Wei Q, Yang Y, Yang Z, Zhang B, Novak J, Renfrow MB, Doria-Rose NA, Koup RA, McDermott AB, Gall JG, Lei QP, Mascola JR, Kwong PD
iScience (2023) 26 pp. 107403-107403 [ Pubmed: 37554450 DOI: doi:10.1016/j.isci.2023.107403 ]
- Hiv-1 env gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Hiv-1 consensus c env trimer with glycan covered base (Complex from Human immunodeficiency virus 1)
- Hiv-1 env gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8g4m
Q-score: 0.564
Wang S, Matassoli F, Zhang B, Liu T, Shen CH, Bylund T, Johnston T, Henry AR, Teng IT, Tripathi P, Becker JE, Changela A, Chaudhary R, Cheng C, Gaudinski M, Gorman J, Harris DR, Lee M, Morano NC, Novik L, O'Dell S, Olia AS, Parchment DK, Rawi R, Roberts-Torres J, Stephens T, Tsybovsky Y, Wang D, Van Wazer DJ, Zhou T, Doria-Rose NA, Koup RA, Shapiro L, Douek DC, McDermott AB, Kwong PD
Cell Rep (2023) 42 pp. 112755-112755 [ DOI: doi:10.1016/j.celrep.2023.112755 Pubmed: 37436899 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelope glycoprotein gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
- Antibody light chain (23 kDa, Protein from Homo sapiens)
- Antibody heavy chain (25 kDa, Protein from Homo sapiens)
- Hiv envelope trimer in complex with three copies of antibody fab (Complex)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8g4t
Q-score: 0.56
Wang S, Matassoli F, Zhang B, Liu T, Shen CH, Bylund T, Johnston T, Henry AR, Teng IT, Tripathi P, Becker JE, Changela A, Chaudhary R, Cheng C, Gaudinski M, Gorman J, Harris DR, Lee M, Morano NC, Novik L, O'Dell S, Olia AS, Parchment DK, Rawi R, Roberts-Torres J, Stephens T, Tsybovsky Y, Wang D, Van Wazer DJ, Zhou T, Doria-Rose NA, Koup RA, Shapiro L, Douek DC, McDermott AB, Kwong PD
Cell Rep (2023) 42 pp. 112755-112755 [ DOI: doi:10.1016/j.celrep.2023.112755 Pubmed: 37436899 ]
- Fab 2c09 light chain (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab 2c09 heavy chain (24 kDa, Protein from Homo sapiens)
- Hiv envelope trimer in complex with three copies of antibody fab (Complex)
- Envelope glycoprotein bg505 ds-sosip gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein bg505 ds-sosip gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
Cryo-EM structure of SARS-CoV-2 spike in complex with FSR22, an anti-SARS-CoV-2 DARPin
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 7tyz
Q-score: 0.391
Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z
Nat Chem Biol (2023) 19 pp. 284-291 [ Pubmed: 36411391 DOI: doi:10.1038/s41589-022-01193-2 ]
- Darpin fsr22 in complex with sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Darpin fsr22 (23 kDa, Protein from Escherichia phage EcSzw-2Escherichia coli)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 7tz0
Q-score: 0.228
Resolution: 4.11 Å
EM Method: Single-particle
Fitted PDBs: 8dw2
Q-score: 0.351
Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z
Nat Chem Biol (2023) 19 pp. 284-291 [ Pubmed: 36411391 DOI: doi:10.1038/s41589-022-01193-2 ]
- Antibody s309 heavy chain (24 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Antibody cr3022 light chain (24 kDa, Protein from Homo sapiens)
- Antibody s309 light chain (23 kDa, Protein from Homo sapiens)
- Darpin sr22 in complex with sars-cov-2 rbd and antibody fabs, s309 and cr3022 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Antibody cr3022 heavy chain (23 kDa, Protein from Homo sapiens)
- Sr22 (16 kDa, Protein from Escherichia phage EcSzw-2)
Resolution: 4.26 Å
EM Method: Single-particle
Fitted PDBs: 8dw3
Q-score: 0.337
Chonira V, Kwon YD, Gorman J, Case JB, Ku Z, Simeon R, Casner RG, Harris DR, Olia AS, Stephens T, Shapiro L, Bender MF, Boyd H, Teng IT, Tsybovsky Y, Krammer F, Zhang N, Diamond MS, Kwong PD, An Z, Chen Z
Nat Chem Biol (2023) 19 pp. 284-291 [ Pubmed: 36411391 DOI: doi:10.1038/s41589-022-01193-2 ]
- Antibody cr3022 heavy chain (23 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Darpin sr16m in complex with sars-cov-2 rbd and antibody fabs, s309 and cr3022 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Antibody s309 light chain (23 kDa, Protein from Homo sapiens)
- Antibody cr3022 light chain (24 kDa, Protein from Homo sapiens)
- Antibody s309 heavy chain (24 kDa, Protein from Homo sapiens)
- Anti-sars-cov-2 darpin sr16m (16 kDa, Protein from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 7tb8
Q-score: 0.41
Zhou T, Wang L, Misasi J, Pegu A, Zhang Y, Harris DR, Olia AS, Talana CA, Yang ES, Chen M, Choe M, Shi W, Teng IT, Creanga A, Jenkins C, Leung K, Liu T, Stancofski ED, Stephens T, Zhang B, Tsybovsky Y, Graham BS, Mascola JR, Sullivan NJ, Kwong PD
Science (2022) 376 pp. eabn8897-eabn8897 [ Pubmed: 35324257 DOI: doi:10.1126/science.abn8897 ]
- The light chain of sars-cov-2 antibody b1-182.1 (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- The light chain of sars-cov-2 antibody a19-61.1 (11 kDa, Protein from Homo sapiens)
- The heavy chain of sars-cov-2 antibody a19-61.1 (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with antibodies b1-182.1 and a19-61.1 (570 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (132 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- The heavy chain of sars-cov-2 antiboddy antibody b1-182.1 (13 kDa, Protein from Homo sapiens)
Locally refined region of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7tbf
Q-score: 0.498
Zhou T, Wang L, Misasi J, Pegu A, Zhang Y, Harris DR, Olia AS, Talana CA, Yang ES, Chen M, Choe M, Shi W, Teng IT, Creanga A, Jenkins C, Leung K, Liu T, Stancofski ED, Stephens T, Zhang B, Tsybovsky Y, Graham BS, Mascola JR, Sullivan NJ, Kwong PD
Science (2022) 376 pp. eabn8897-eabn8897 [ Pubmed: 35324257 DOI: doi:10.1126/science.abn8897 ]
- Heavy chain of sars-cov-2 antibody b1-182.1 (24 kDa, Protein from Homo sapiens)
- Spike glycoprotein (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of sars-cov-2 antibody a19-61.1 (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike in complex with antibodies b1-182.1 and a19-61.1 (570 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of sars-cov-2 antibody b1-182.1 (23 kDa, Protein from Homo sapiens)
- Heavy chain of sars-cov-2 antibody a19-61.1 (13 kDa, Protein from Homo sapiens)