Structure of a group II intron ribonucleoprotein in the pre-ligation (pre-2F) state
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8t2r
Q-score: 0.459
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Calcium ion (40 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- 5'exon (2 kDa, RNA from [Eubacterium] rectale)
- Intron (208 kDa, RNA from [Eubacterium] rectale)
- Intron rnp complex in pre-2f (300 kDa, Complex from [Eubacterium] rectale)
Structure of a group II intron ribonucleoprotein in the pre-branching (pre-1F) state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8t2s
Q-score: 0.48
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Intron rnp complex in pre-1f (300 kDa, Complex from [Eubacterium] rectale)
- Calcium ion (40 Da, Ligand)
- Ammonium ion (18 Da, Ligand)
- Rna (551-mer) (211 kDa, RNA from [Eubacterium] rectale)
Structure of a group II intron ribonucleoprotein in the post-ligation (post-2F) state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8t2t
Q-score: -0.023
Nature (2023) 624 pp. 682-688 [ DOI: doi:10.1038/s41586-023-06746-6 Pubmed: 37993708 ]
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Magnesium ion (24 Da, Ligand)
- Rna (537-mer) (206 kDa, RNA from [Eubacterium] rectale)
- Intron rnp complex in post-2f (300 kDa, Complex from [Eubacterium] rectale)
- Ammonium ion (18 Da, Ligand)
- Rna (5'-r(p*up*up*up*cp*up*up*up*up*g)-3') (2 kDa, RNA from [Eubacterium] rectale)
Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8euu
Q-score: 0.545
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 [ DOI: doi:10.1038/s41467-023-42098-5 Pubmed: 37989731 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Vrc34.01 fab variable heavy chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Vrc34.01 fab variable light chain (23 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip vrc34.01 fab complex (Complex from Human immunodeficiency virus 1)
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 [ DOI: doi:10.1038/s41467-023-42098-5 Pubmed: 37989731 ]
- Water (18 Da, Ligand)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Vrc34.01-combo1 fab variable light chain (23 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip vrc34.01-combo1 fab complex (Complex from Human immunodeficiency virus 1)
- 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 [ DOI: doi:10.1038/s41467-023-42098-5 Pubmed: 37989731 ]
- Vrc34.01-mm28 fab variable light chain (23 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Envelope glycoprotein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bg505 ds-sosip vrc34.01-mm28 fab complex (Complex from Human immunodeficiency virus 1)
- Vrc34.01-mm28 fab variable heavy chain (23 kDa, Protein from Homo sapiens)
Western Equine Encephalitis Virus-Like Particle in Complex with SKW19 Fab
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 ]
Western Equine Encephalitis Virus-Like Particle in Complex with SKW24 Fab
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 ]
Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
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 ]
Lassa GPC trimer in complex with Fab GP23
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 ]