Venezuelan equine encephalitis virus-like particle in complex with Fab SKT05, local refinement
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8eeu
Q-score: 0.462
Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG, Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M, Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schon A, Schramm CA, Shen CH, Shi W, Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong PD, Roederer M
Cell (2023) 186 pp. 2672-2689.e25 [ DOI: doi:10.1016/j.cell.2023.05.019 Pubmed: 37295404 ]
- Fab skt05 heavy chain (25 kDa, Protein from Macaca fascicularis)
- Fab skt05 light chain (23 kDa, Protein from Macaca fascicularis)
- Coat protein (138 kDa, Protein from Venezuelan equine encephalitis virus)
- Complex between venezuelan equine encephalitis virus-like particle and fab skt05 (33 MDa, Complex from Venezuelan equine encephalitis virus)
Venezuelan equine encephalitis virus-like particle in complex with Fab SKT-20, local refinement
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8eev
Q-score: 0.44
Sutton MS, Pletnev S, Callahan V, Ko S, Tsybovsky Y, Bylund T, Casner RG, Cerutti G, Gardner CL, Guirguis V, Verardi R, Zhang B, Ambrozak D, Beddall M, Lei H, Yang ES, Liu T, Henry AR, Rawi R, Schon A, Schramm CA, Shen CH, Shi W, Stephens T, Yang Y, Florez MB, Ledgerwood JE, Burke CW, Shapiro L, Fox JM, Kwong PD, Roederer M
Cell (2023) 186 pp. 2672-2689.e25 [ DOI: doi:10.1016/j.cell.2023.05.019 Pubmed: 37295404 ]
- Fab skt20 light chain (23 kDa, Protein from Macaca fascicularis)
- Fab skt20 heavy chain (25 kDa, Protein from Macaca fascicularis)
- Coat protein (138 kDa, Protein from Venezuelan equine encephalitis virus)
- Complex between venezuelan equine encephalitis virus-like particle and fab skt20 (33 MDa, Complex from Venezuelan equine encephalitis virus)
SARS-CoV-2 spike trimer in complex with Fab NE12, ensemble map
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- Sars-cov-2 s6p spike trimer (Protein from Severe acute respiratory syndrome coronavirus 2)
- Ne12 fab light chain (Protein from Homo sapiens)
- Ne12 fab heavy chain (Protein from Homo sapiens)
- Sars-cov-2 s6p spike trimer in complex with fab ne12 (580 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike trimer in complex with Fab NE12, local refinement map
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7u9o
Q-score: 0.518
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ne12 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Ne12 fab light chain (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike receptor-binding domain in complex with fab ne12 (110 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike trimer in complex with Fab NA8, ensemble map
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- Sars-cov-2 s6p spike trimer (Protein from Severe acute respiratory syndrome coronavirus 2)
- Na8 fab heavy chain (Protein from Homo sapiens)
- Na8 fab light chain (Protein from Homo sapiens)
- Sars-cov-2 s6p spike trimer in complex with fab na8 (580 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 spike trimer in complex with Fab NA8, local refinement map
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7u9p
Q-score: 0.528
Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P
Cell Rep (2022) 41 pp. 111528-111528 [ Pubmed: 36302375 DOI: doi:10.1016/j.celrep.2022.111528 ]
- Sars-cov-2 spike receptor-binding domain in complex with fab na8 (110 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Na8 fab light chain (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Na8 fab heavy chain (24 kDa, Protein from Homo sapiens)
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 Env
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7n28
Q-score: 0.385
Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria-Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F
Adv Sci (2022) 9 pp. e2200063-e2200063 [ DOI: doi:10.1002/advs.202200063 Pubmed: 35319830 ]
- Phosphate ion (94 Da, Ligand)
- A complex of hiv-1 env with antibodies 3bnc117 and j033 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 3bnc117 antibody heavy chain (24 kDa, Protein from Homo sapiens)
- 3bnc117 antibody light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- J033 antibody heavy chain (24 kDa, Protein from Macaca mulatta)
- J033 antibody light chain (23 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp41 (19 kDa, Protein from Human immunodeficiency virus 1)
- Alpha-d-mannopyranose (180 Da, Ligand)
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7mxd
Q-score: 0.47
Gao N, Gai Y, Meng L, Wang C, Wang W, Li X, Gu T, Louder MK, Doria-Rose NA, Wiehe K, Nazzari AF, Olia AS, Gorman J, Rawi R, Wu W, Smith C, Khant H, de Val N, Yu B, Luo J, Niu H, Tsybovsky Y, Liao H, Kepler TB, Kwong PD, Mascola JR, Qin C, Zhou T, Yu X, Gao F
Adv Sci (2022) 9 pp. e2200063-e2200063 [ DOI: doi:10.1002/advs.202200063 Pubmed: 35319830 ]
- Phosphate ion (94 Da, Ligand)
- J038 antibody heavy chain (24 kDa, Protein from Macaca mulatta)
- J038 antibody light chain (23 kDa, Protein from Macaca mulatta)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- 3bnc117 antibody heavy chain (24 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 3bnc117 antibody light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- A complex of hiv-1 env with antibodies 3bnc117 and j038 (Complex from Homo sapiens)
Structure of freshly purified SARS-CoV-2 S2P spike at pH 7.4
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7mtc
Q-score: 0.6
Olia AS, Tsybovsky Y, Chen SJ, Liu C, Nazzari AF, Ou L, Wang L, Kong WP, Leung K, Liu T, Stephens T, Teng IT, Wang S, Yang ES, Zhang B, Zhang Y, Zhou T, Mascola JR, Kwong PD
J Biol Chem (2021) 297 pp. 101127-101127 [ Pubmed: 34461095 DOI: doi:10.1016/j.jbc.2021.101127 ]
Structure of aged SARS-CoV-2 S2P spike at pH 7.4
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7mtd
Q-score: 0.443
Olia AS, Tsybovsky Y, Chen SJ, Liu C, Nazzari AF, Ou L, Wang L, Kong WP, Leung K, Liu T, Stephens T, Teng IT, Wang S, Yang ES, Zhang B, Zhang Y, Zhou T, Mascola JR, Kwong PD
J Biol Chem (2021) 297 pp. 101127-101127 [ Pubmed: 34461095 DOI: doi:10.1016/j.jbc.2021.101127 ]