HIV-1 intasome core bound with DTG
Resolution: 2.01 Å
EM Method: Single-particle
Fitted PDBs: 9c9m
Q-score: 0.548
Li M, Li Z, Chen X, Cui Y, Engelman AN, Craigie R
Viruses (2024) 16 [ Pubmed: 39066328 DOI: doi:10.3390/v16071166 ]
- (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)
- Zinc ion (65 Da, Ligand)
- Integrase (12 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 intasomes core (Complex from Human immunodeficiency virus 1)
- Vdna (7 kDa, DNA from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Integrase (39 kDa, Protein from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Viral dna (8 kDa, DNA from Human immunodeficiency virus 1)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8w09
Q-score: 0.461
Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R
J Mol Biol (2024) 436 pp. 168557-168557 [ DOI: doi:10.1016/j.jmb.2024.168557 Pubmed: 38582148 ]
- Vdna (27 kDa, DNA from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Wild-type hiv-1 intasomes (400 kDa, Complex from Human immunodeficiency virus 1)
- Vdna (8 kDa, DNA from Human immunodeficiency virus 1)
- Integrase (32 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)
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8w2r
Q-score: 0.432
Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R
J Mol Biol (2024) 436 pp. 168557-168557 [ DOI: doi:10.1016/j.jmb.2024.168557 Pubmed: 38582148 ]
- (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)
- Zinc ion (65 Da, Ligand)
- Hiv-1 p5-in intasomes core (Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(*ap*cp*tp*gp*cp*tp*ap*gp*ap*gp*ap*tp*tp*tp*tp*cp*cp*cp*g)-3') (8 kDa, DNA from synthetic construct)
- Dna (5'-d(p*cp*gp*gp*gp*ap*ap*ap*ap*tp*cp*tp*cp*tp*ap*gp*cp*a)-3') (7 kDa, DNA from synthetic construct)
- Integrase (39 kDa, Protein from Human immunodeficiency virus 1)
HIV-1 intasome core assembled with wild-type integrase, 1F
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8w34
Q-score: 0.236
Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R
J Mol Biol (2024) 436 pp. 168557-168557 [ DOI: doi:10.1016/j.jmb.2024.168557 Pubmed: 38582148 ]
- Zinc ion (65 Da, Ligand)
- Integrase (32 kDa, Protein from Human immunodeficiency virus 1)
- Dna (5'-d(p*gp*tp*gp*gp*ap*ap*ap*ap*tp*cp*tp*cp*tp*ap*gp*cp*a)-3') (8 kDa, DNA from synthetic construct)
- 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)
- Dna (5'-d(*ap*cp*tp*gp*cp*tp*ap*gp*ap*gp*ap*tp*tp*tp*tp*cp*cp*ap*c)-3') (27 kDa, DNA from synthetic construct)
- Hiv-1 wild-type conserved intasomes core (Complex from Human immunodeficiency virus 1)
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)