Structure of WT HIV-1 intasome bound to Dolutegravir
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8fn7
Q-score: 0.552
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Wt hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of E138K HIV-1 intasome with Dolutegravir bound
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8fnd
Q-score: 0.48
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Wt hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of E138K HIV-1 intasome with Dolutegravir bound
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8fng
Q-score: 0.625
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- G140a hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of Q148K HIV-1 intasome with Dolutegravir bound
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8fnh
Q-score: 0.587
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of E138K/G140A HIV-1 intasome with Dolutegravir bound
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8fnj
Q-score: 0.586
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- E138k/g140a hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8fnl
Q-score: 0.605
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- E138k/q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of G140A/Q148K HIV-1 intasome with Dolutegravir bound
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8fnm
Q-score: 0.549
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- G140a/q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
Structure of E138K/G140A/Q148K HIV-1 intasome with Dolutegravir bound
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8fnn
Q-score: 0.582
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- E138k/g140a/q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
Structure of E138K/G140A/Q148R HIV-1 intasome with Dolutegravir bound
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8fno
Q-score: 0.601
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- E138k/g140a/q148r hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)
Structure of E138K/G140S/Q148H HIV-1 intasome with Dolutegravir bound
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8fnp
Q-score: 0.644
Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D
Sci Adv (2023) 9 pp. eadg5953-eadg5953 [ DOI: doi:10.1126/sciadv.adg5953 Pubmed: 37478179 ]
- Zinc ion (65 Da, Ligand)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- E138k/g140s/q148h hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- (4r,12as)-n-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2h-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide (419 Da, Ligand)
- Water (18 Da, Ligand)