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 ]
- Target_val (21 kDa, DNA from Peltigera membranacea)
- Tnsd (52 kDa, Protein from Peltigera membranacea)
- Tnsc (43 kDa, Protein from Peltigera membranacea)
- Integrase (103 kDa, Protein from Peltigera membranacea)
- Water (18 Da, Ligand)
- Tnsabcd (Complex from Peltigera membranacea)
- Dna (Complex from Peltigera membranacea)
- Trna_le_luego (48 kDa, DNA from Peltigera membranacea)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tnsabcd-dna complex (Complex)
- Le_polya (26 kDa, DNA from Peltigera membranacea)
- Re_target (61 kDa, DNA from Peltigera membranacea)
- Re_polya (53 kDa, DNA from Peltigera membranacea)
- Zinc ion (65 Da, Ligand)
- Target_downstream (11 kDa, DNA from Peltigera membranacea)
Sasnauskas G, Gaizauskaite U, Tamulaitiene G
To Be Published
- Crispr-associated endoribonuclease cas2 (13 kDa, Protein from Streptococcus thermophilus DGCC 7710)
- Integration target, chain j (14 kDa, DNA from synthetic construct)
- Cas1-cas2 crispr integrase bound to prespacer and target dna, streptococcus thermophilus dgcc 7710 crispr3 system (Complex from Streptococcus thermophilus DGCC 7710)
- Magnesium ion (24 Da, Ligand)
- Integration target, chain i (14 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas1 (35 kDa, Protein from Streptococcus thermophilus DGCC 7710)
- Prespacer dna, chain g (8 kDa, DNA from synthetic construct)
- Prespacer dna, chain h (7 kDa, DNA from synthetic construct)
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)
- Water (18 Da, Ligand)
- Integrase (39 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)
- Viral dna (8 kDa, DNA from Human immunodeficiency virus 1)
- Zinc ion (65 Da, Ligand)
- Integrase (12 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.17 Å
EM Method: Single-particle
Fitted PDBs: 8pk1
Q-score: 0.463
Sasnauskas G, Gaizauskaite U, Tamulaitiene G
To Be Published
- Cas1-cas2 crispr integrase-prespacer dna complex (Complex from Streptococcus thermophilus DGCC 7710)
- Crispr-associated endoribonuclease cas2 (13 kDa, Protein from Streptococcus thermophilus DGCC 7710)
- Chains: g,j (7 kDa, DNA from synthetic construct)
- Chains: h,k (8 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease cas1 (35 kDa, Protein from Streptococcus thermophilus DGCC 7710)
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 [ Pubmed: 38582148 DOI: doi:10.1016/j.jmb.2024.168557 ]
- (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 (32 kDa, Protein from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Vdna (8 kDa, DNA from Human immunodeficiency virus 1)
- Wild-type hiv-1 intasomes (400 kDa, Complex from Human immunodeficiency virus 1)
- Vdna (27 kDa, DNA 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 ]
- (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*cp*g)-3') (8 kDa, DNA from synthetic construct)
- 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(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 [ Pubmed: 38582148 DOI: doi:10.1016/j.jmb.2024.168557 ]
- Integrase (32 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 wild-type conserved intasomes core (Complex from Human immunodeficiency virus 1)
- 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)
- (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)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 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)
Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex in activated state
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8fti
Q-score: 0.411
Deng X, Osikpa E, Yang J, Oladeji SJ, Smith J, Gao X, Gao Y
Nat Commun (2023) 14 pp. 5845-5845 [ DOI: doi:10.1038/s41467-023-41501-5 Pubmed: 37730702 ]
- Crrna-linker-target hairpin rna (Complex)
- Integrase (Complex)
- Crrna-linker-target hairpin rna (33 kDa, RNA from synthetic construct)
- Integrase (90 kDa, Protein from Planctomycetota bacterium)
- Ternary complex of cas13bt3 in complex with crrna and 30 nt target rna (123 kDa, Complex from Planctomycetota bacterium)
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 leader and repeat, anti-sense strand of dna (52 kDa, DNA from Pseudomonas aeruginosa PA14)
- Ihf heterodimer (Complex from Pseudomonas aeruginosa PA14)
- Cas1-cas2/3 integrase and ihf bound to crispr leader, repeat and foreign dna (122 kDa, Complex)
- Crispr-associated endonuclease cas1 (38 kDa, Protein from Pseudomonas aeruginosa PA14)
- Integration host factor subunit beta (10 kDa, Protein from Pseudomonas aeruginosa PA14)
- 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, sense strand of dna (42 kDa, DNA from Pseudomonas aeruginosa PA14)
- Prespacer, anti-sense strand of dna (8 kDa, DNA from synthetic construct)
- Crispr repeat and prespacer, sense strand of dna (18 kDa, DNA from synthetic construct)
- Crispr leader, repeat, and prespacer dna annealed to mimic a half-site integration intermediate. (Complex)
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 ]
- Water (18 Da, Ligand)
- 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)
- Magnesium ion (24 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)
- Zinc ion (65 Da, Ligand)