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 [ DOI: doi:10.3390/v16071166 Pubmed: 39066328 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Integrase (12 kDa, Protein from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Viral dna (8 kDa, DNA from Human immunodeficiency virus 1)
- (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)
- Integrase (39 kDa, Protein from Human immunodeficiency virus 1)
- Vdna (7 kDa, DNA from Human immunodeficiency virus 1)
- Hiv-1 intasomes core (Complex from Human immunodeficiency virus 1)
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 [ Pubmed: 38582148 DOI: doi:10.1016/j.jmb.2024.168557 ]
- 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)
- Hiv-1 p5-in intasomes core (Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- 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)
- Zinc ion (65 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)
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 [ Pubmed: 38582148 DOI: doi:10.1016/j.jmb.2024.168557 ]
- 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)
- Integrase (32 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- 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)
- Hiv-1 wild-type conserved intasomes core (Complex from Human immunodeficiency virus 1)
- Zinc ion (65 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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Wt hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- (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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Wt hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Dna (27-mer) (8 kDa, DNA from Human immunodeficiency virus 1)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- (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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- G140a 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)
- 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)
- (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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- 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)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- (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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- E138k/g140a hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna (25-mer) (7 kDa, DNA from Human immunodeficiency virus 1)
- (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)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 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)
- (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)
- E138k/q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
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 [ Pubmed: 37478179 DOI: doi:10.1126/sciadv.adg5953 ]
- Magnesium ion (24 Da, Ligand)
- G140a/q148k hiv-1 intasome bound to dolutegravir (500 kDa, Complex from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Lamina-associated polypeptide 2, isoform alpha,integrase chimera (39 kDa, Protein from Human immunodeficiency virus 1)
- 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)
- (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)