Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 9bw1
Q-score: 0.349
Wang S, Siddique R, Hall MC, Rice PA, Chang L
Cell (2024) 187 pp. 6865- [ DOI: doi:10.1016/j.cell.2024.09.023 Pubmed: 39383864 ]
- Trna_le_luego (48 kDa, DNA from Peltigera membranacea)
- Zinc ion (65 Da, Ligand)
- Tnsabcd-dna complex (Complex)
- Target_val (21 kDa, DNA from Peltigera membranacea)
- Tnsc (43 kDa, Protein from Peltigera membranacea)
- Tnsabcd (Complex from Peltigera membranacea)
- Target_downstream (11 kDa, DNA from Peltigera membranacea)
- Tnsd (52 kDa, Protein from Peltigera membranacea)
- Le_polya (26 kDa, DNA from Peltigera membranacea)
- Re_polya (53 kDa, DNA from Peltigera membranacea)
- Dna (Complex from Peltigera membranacea)
- Integrase (103 kDa, Protein from Peltigera membranacea)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Re_target (61 kDa, DNA from Peltigera membranacea)
- Water (18 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 [ 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)
Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 8flj
Q-score: 0.35
Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B
Nat Struct Mol Biol (2023) 30 pp. 1675-1685 [ DOI: doi:10.1038/s41594-023-01097-2 Pubmed: 37710013 ]
- Crispr repeat and prespacer, sense strand of dna (18 kDa, DNA from synthetic construct)
- Cas1-cas2/3 heterohexameric integrase (Complex from Pseudomonas aeruginosa PA14)
- Crispr-associated nuclease/helicase cas3 subtype i-f/ypest (121 kDa, Protein from Pseudomonas aeruginosa PA14)
- Integration host factor subunit alpha (11 kDa, Protein from Pseudomonas aeruginosa PA14)
- Crispr leader, repeat, and prespacer dna annealed to mimic a half-site integration intermediate. (Complex)
- Ihf heterodimer (Complex from Pseudomonas aeruginosa PA14)
- Cas1-cas2/3 integrase and ihf bound to crispr leader, repeat and foreign dna (122 kDa, Complex)
- Integration host factor subunit beta (10 kDa, Protein from Pseudomonas aeruginosa PA14)
- Crispr leader, sense strand of dna (42 kDa, DNA from Pseudomonas aeruginosa PA14)
- Crispr leader and repeat, anti-sense strand of dna (52 kDa, DNA from Pseudomonas aeruginosa PA14)
- Crispr-associated endonuclease cas1 (38 kDa, Protein from Pseudomonas aeruginosa PA14)
- Prespacer, anti-sense strand of dna (8 kDa, DNA from synthetic construct)
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)