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)
Mouse mammary tumor virus strand transfer complex intasome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7usf
Q-score: 0.403
Jozwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D
Nucleic Acids Res (2022) 50 pp. 8898-8918 [ Pubmed: 35947647 DOI: doi:10.1093/nar/gkac644 ]
- Vdna strand (non-transferred) (9 kDa, DNA from Mouse mammary tumor virus)
- Zinc ion (65 Da, Ligand)
- Vdna-tdna strand (transferred) (12 kDa, DNA from Mouse mammary tumor virus)
- Mmtv strand transfer complex intasome (300 kDa, Complex from Mouse mammary tumor virus)
- Integrase (35 kDa, Protein from Mouse mammary tumor virus)
- Calcium ion (40 Da, Ligand)
- Tdna strand (4 kDa, DNA from Mouse mammary tumor virus)
Higher-order assembly of multiple MMTV strand transfer complex intasomes
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7ut1
Q-score: 0.39
Jozwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D
Nucleic Acids Res (2022) 50 pp. 8898-8918 [ Pubmed: 35947647 DOI: doi:10.1093/nar/gkac644 ]
- Zinc ion (65 Da, Ligand)
- Vdna-tdna strand (transferred) (12 kDa, DNA from Mouse mammary tumor virus)
- Higher-order assembly of multiple mmtv strand transfer complex intasomes (600 kDa, Complex from Mouse mammary tumor virus)
- Integrase (35 kDa, Protein from Mouse mammary tumor virus)
- Vdna strand (non-transferred) (6 kDa, DNA from Mouse mammary tumor virus)
- Tdna strand (4 kDa, DNA from Mouse mammary tumor virus)
MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7z1z
Q-score: 0.19
Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P
Nat Commun (2022) 13 pp. 2416- [ DOI: doi:10.1038/s41467-022-29928-8 ]
- Pol polyprotein (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Dna (37-mer) (15 kDa, DNA from DNA molecule)
- Dna (5'-d(*gp*cp*tp*gp*cp*gp*ap*gp*ap*tp*cp*cp*gp*cp*tp*cp*cp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)
- Zinc ion (65 Da, Ligand)
- Mvv stc intasome in complex with ledgf (480 kDa, Complex from Visna/maedi virus EV1 KV1772)
- Pc4 and sfrs1-interacting protein (11 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*tp*tp*gp*ap*tp*tp*ap*gp*gp*gp*tp*g)-3') (7 kDa, DNA from DNA molecule)
MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 7u32
Q-score: 0.256
Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P
Nat Commun (2022) 13 pp. 2416-2416 [ Pubmed: 35504909 DOI: doi:10.1038/s41467-022-29928-8 ]
- Dna ev273 (8 kDa, DNA from synthetic construct)
- Mvv cleaved synaptic complex intasome (480 kDa, Complex from Streptomyces griseus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Integrase (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Dna ev272 (8 kDa, DNA from synthetic construct)
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 7jn3
Q-score: 0.328
Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP
Commun Biol (2021) 4 pp. 330-330 [ Pubmed: 33712691 DOI: doi:10.1038/s42003-021-01855-2 ]
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(*ap*ap*tp*gp*tp*tp*gp*tp*cp*tp*tp*ap*tp*gp*cp*ap*ap*t)-3') (5 kDa, DNA from Rous sarcoma virus (strain Schmidt-Ruppin A))
- Zinc ion (65 Da, Ligand)
- Cleaved synaptic complex (csc) formed with rous sarcoma virus integrase and viral dna in presence of hiv-1 integrase strand inhibitor mk-2048 (257 kDa, Complex from Rous sarcoma virus (strain Schmidt-Ruppin A))
- Dna (5'-d(*ap*tp*tp*gp*cp*ap*tp*ap*ap*gp*ap*cp*ap*ap*cp*a)-3') (4 kDa, DNA from Rous sarcoma virus (strain Schmidt-Ruppin A))
- (6s)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-n,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide (461 Da, Ligand)
- Integrase (30 kDa, Protein from Rous sarcoma virus (strain Schmidt-Ruppin A))
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ku7
Q-score: 0.185
Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP
Commun Biol (2021) 4 pp. 330-330 [ Pubmed: 33712691 DOI: doi:10.1038/s42003-021-01855-2 ]
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(*ap*ap*tp*gp*tp*tp*gp*tp*cp*tp*tp*ap*tp*gp*cp*ap*ap*t)-3') (5 kDa, DNA from Rous sarcoma virus (strain Schmidt-Ruppin A))
- Zinc ion (65 Da, Ligand)
- Cleaved synaptic complex (csc) formed with rous sarcoma virus integrase and viral dna in presence of hiv-1 integrase strand inhibitor mk-2048 (257 kDa, Complex from Rous sarcoma virus (strain Schmidt-Ruppin A))
- Dna (5'-d(*ap*tp*tp*gp*cp*ap*tp*ap*ap*gp*ap*cp*ap*ap*cp*a)-3') (4 kDa, DNA from Rous sarcoma virus (strain Schmidt-Ruppin A))
- (6s)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-n,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide (461 Da, Ligand)
- Integrase (30 kDa, Protein from Rous sarcoma virus (strain Schmidt-Ruppin A))
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 6rwl
Q-score: 0.471
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P
Science (2020) 367 pp. 806-810 [ Pubmed: 32001525 DOI: doi:10.1126/science.aay4919 ]
- Sivrcm intasome in complex with bictegravir (Complex)
- Dna (5'-d(p*gp*cp*tp*ap*ap*gp*ap*ap*ap*ap*ap*tp*cp*tp*cp*tp*ap*cp*cp*a)-3') (9 kDa, DNA from Simian immunodeficiency virus)
- Pol protein (32 kDa, Protein from Simian immunodeficiency virus)
- Pol protein (32 kDa, Protein from Simian immunodeficiency virus)
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(*ap*ap*cp*tp*gp*gp*tp*ap*gp*ap*gp*ap*tp*tp*tp*tp*tp*cp*tp*tp*ap*gp*c)-3') (10 kDa, DNA from Simian immunodeficiency virus)
- Pol protein (32 kDa, Protein from Simian immunodeficiency virus)
- Pol protein (Complex from Simian immunodeficiency virus)
- Dna (Complex from Simian immunodeficiency virus)
SIVrcm intasome in complex with bictegravir
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 6rwm
Q-score: 0.563
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P
Science (2020) 367 pp. 806-810 [ Pubmed: 32001525 DOI: doi:10.1126/science.aay4919 ]
- Sivrcm intasome in complex with bictegravir (Complex)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Dna (5'-d(p*gp*cp*tp*ap*ap*gp*ap*ap*ap*ap*ap*tp*cp*tp*cp*tp*ap*cp*cp*a)-3') (9 kDa, DNA from Simian immunodeficiency virus)
- Pol protein (32 kDa, Protein from Simian immunodeficiency virus)
- Zinc ion (65 Da, Ligand)
- Bictegravir (449 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Dna (5'-d(*ap*ap*cp*tp*gp*gp*tp*ap*gp*ap*gp*ap*tp*tp*tp*tp*tp*cp*tp*tp*ap*gp*c)-3') (10 kDa, DNA from Simian immunodeficiency virus)
- Pol protein (Complex from Simian immunodeficiency virus)
- Dna (Complex from Simian immunodeficiency virus)
SIVrcm intasome in complex with dolutegravir
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6rwn
Q-score: 0.524
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P
Science (2020) 367 pp. 806-810 [ Pubmed: 32001525 DOI: doi:10.1126/science.aay4919 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 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(p*gp*cp*tp*ap*ap*gp*ap*ap*ap*ap*ap*tp*cp*tp*cp*tp*ap*cp*cp*a)-3') (9 kDa, DNA from Simian immunodeficiency virus)
- Pol protein (32 kDa, Protein from Simian immunodeficiency virus)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Dna (5'-d(*ap*ap*cp*tp*gp*gp*tp*ap*gp*ap*gp*ap*tp*tp*tp*tp*tp*cp*tp*tp*ap*gp*c)-3') (10 kDa, DNA from Simian immunodeficiency virus)
- Dna (Complex from Simian immunodeficiency virus)
- Sivrcm intasome in complex with dolutegravir (Complex)
- Pol protein (Complex from Simian immunodeficiency virus)