Venezuelan equine encephalitis virus-like particle in complex with Fab SKT20
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 ]
- Complex between venezuelan equine encephalitis virus-like particle and fab skt20 (33 MDa, Complex from Venezuelan equine encephalitis virus)
- Fab skt20 light chain (Protein from Macaca fascicularis)
- Fab skt20 heavy chain (Protein from Macaca fascicularis)
- Coat protein (Protein 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 ]
- Complex between venezuelan equine encephalitis virus-like particle and fab skt20 (33 MDa, Complex from Venezuelan equine encephalitis virus)
- Fab skt20 heavy chain (25 kDa, Protein from Macaca fascicularis)
- Coat protein (138 kDa, Protein from Venezuelan equine encephalitis virus)
- Fab skt20 light chain (23 kDa, Protein from Macaca fascicularis)
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 [ Pubmed: 37436899 DOI: doi:10.1016/j.celrep.2023.112755 ]
- Envelope glycoprotein bg505 ds-sosip gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Fab 2c09 heavy chain (24 kDa, Protein from Homo sapiens)
- Envelope glycoprotein bg505 ds-sosip gp120 (52 kDa, Protein from Human immunodeficiency virus 1)
- Fab 2c09 light chain (23 kDa, Protein from Homo sapiens)
- Hiv envelope trimer in complex with three copies of antibody fab (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Ligand-free Lassa GPC Trimer with C3 Symmetry
Gorman J, Cheung CS, Duan Z, Ou L, Wang M, Chen X, Cheng C, Biju A, Sun Y, Wang P, Yang Y, Zhang B, Boyington JC, Bylund T, Charaf S, Chen SJ, Du H, Henry AR, Liu T, Sarfo EK, Schramm CA, Shen CH, Stephens T, Teng IT, Todd JP, Tsybovsky Y, Verardi R, Wang D, Wang S, Wang Z, Zheng CY, Zhou T, Douek DC, Mascola JR, Ho DD, Ho M, Kwong PD
Nat Commun (2024) 15 pp. 285-285 [ DOI: doi:10.1038/s41467-023-44534-y Pubmed: 38177144 ]
- Lassa gpc (Protein from Lassa virus Josiah)
- Lassa gpc trimer (Complex from Lassa virus Josiah)
Ligand-free Lassa GPC Trimer with C1 Symmetry
Gorman J, Cheung CS, Duan Z, Ou L, Wang M, Chen X, Cheng C, Biju A, Sun Y, Wang P, Yang Y, Zhang B, Boyington JC, Bylund T, Charaf S, Chen SJ, Du H, Henry AR, Liu T, Sarfo EK, Schramm CA, Shen CH, Stephens T, Teng IT, Todd JP, Tsybovsky Y, Verardi R, Wang D, Wang S, Wang Z, Zheng CY, Zhou T, Douek DC, Mascola JR, Ho DD, Ho M, Kwong PD
Nat Commun (2024) 15 pp. 285-285 [ DOI: doi:10.1038/s41467-023-44534-y Pubmed: 38177144 ]
P. berghei kinesin-8B motor domain in AMPPNP state bound to tubulin dimer
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7z2b
Q-score: 0.367
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA
Nat Commun (2022) 13 pp. 6988-6988 [ DOI: doi:10.1038/s41467-022-34710-x Pubmed: 36384964 ]
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- P. berghei kinesin-8b motor domain in amppnp state bound to tubulin dimer (Complex from Plasmodium berghei)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Kinesin-8, putative (38 kDa, Protein from Plasmodium berghei)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
P. berghei kinesin-8B motor domain in no nucleotide state bound to tubulin dimer
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 7z2a
Q-score: 0.253
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA
Nat Commun (2022) 13 pp. 6988-6988 [ DOI: doi:10.1038/s41467-022-34710-x Pubmed: 36384964 ]
- Kinesin-8, putative (39 kDa, Protein from Plasmodium berghei)
- P. berghei kinesin-8b motor domain in no nucleotide state bound to tubulin dimer (Complex from Plasmodium berghei)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
P. falciparum kinesin-8B motor domain in no nucleotide bound to tubulin dimer
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 7z2c
Q-score: 0.296
Liu T, Shilliday F, Cook AD, Zeeshan M, Brady D, Tewari R, Sutherland CJ, Roberts AJ, Moores CA
Nat Commun (2022) 13 pp. 6988-6988 [ DOI: doi:10.1038/s41467-022-34710-x Pubmed: 36384964 ]
- Kinesin-like protein (39 kDa, Protein from Plasmodium falciparum)
- Tubulin beta chain (47 kDa, Protein from Sus scrofa)
- P. falciparum kinesin-8b motor domain in no nucleotide state bound to tubulin dimer (Complex from Plasmodium berghei)
- Magnesium ion (24 Da, Ligand)
- Detyrosinated tubulin alpha-1b chain (47 kDa, Protein from Sus scrofa)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 7d10
Q-score: 0.501
Zhang S, Zhou J, Zhang Y, Liu T, Friedel P, Zhuo W, Somasekharan S, Roy K, Zhang L, Liu Y, Meng X, Deng H, Zeng W, Li G, Forbush B, Yang M
Commun Biol (2021) 4 pp. 226-226 [ Pubmed: 33597714 DOI: doi:10.1038/s42003-021-01750-w ]
- Palmitic acid (256 Da, Ligand)
- Solute carrier family 12 member 2 (131 kDa, Protein from Homo sapiens)
- Human nkcc1 (Complex from Homo sapiens)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7d14
Q-score: 0.472
Zhang S, Zhou J, Zhang Y, Liu T, Friedel P, Zhuo W, Somasekharan S, Roy K, Zhang L, Liu Y, Meng X, Deng H, Zeng W, Li G, Forbush B, Yang M
Commun Biol (2021) 4 pp. 226-226 [ Pubmed: 33597714 DOI: doi:10.1038/s42003-021-01750-w ]
- Mouse kcc2 (Cellular component from Mus musculus)
- Solute carrier family 12 member 5 (126 kDa, Protein from Mus musculus)