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)
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 [ DOI: doi:10.1093/nar/gkac644 Pubmed: 35947647 ]
- Mmtv strand transfer complex intasome (300 kDa, Complex from Mouse mammary tumor virus)
- Integrase (35 kDa, Protein from Mouse mammary tumor virus)
- Zinc ion (65 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Vdna-tdna strand (transferred) (12 kDa, DNA from Mouse mammary tumor virus)
- Vdna strand (non-transferred) (9 kDa, DNA from Mouse mammary tumor virus)
- Tdna strand (4 kDa, DNA from Mouse mammary tumor virus)
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 ]
- Zinc ion (65 Da, Ligand)
- Integrase (30 kDa, Protein 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)
- 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))
- 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))
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 ]
- Zinc ion (65 Da, Ligand)
- Integrase (30 kDa, Protein 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)
- 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))
- 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))
Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8)
Resolution: 4.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 6skn
Q-score: 0.249
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6y9v
Q-score: 0.155
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
- Hiv-1 capsid (Complex from Human immunodeficiency virus 1)
- Gag-pol polyprotein (24 kDa, Protein from Human immunodeficiency virus 1)
- Peptidyl-prolyl cis-trans isomerase a (17 kDa, Protein from Homo sapiens)
- In vitro assembled hiv-1 capsid in tubular assembly (Complex)
- Cyclophilin a (Complex from Homo sapiens)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6y9w
Q-score: 0.274
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
- Hiv-1 capsid (Complex from Human immunodeficiency virus 1)
- Gag-pol polyprotein (24 kDa, Protein from Human immunodeficiency virus 1)
- Peptidyl-prolyl cis-trans isomerase a (17 kDa, Protein from Homo sapiens)
- In vitro assembled hiv-1 capsid in tubular assembly (Complex)
- Cyclophilin a (Complex from Homo sapiens)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6y9x
Q-score: 0.219
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
- Hiv-1 capsid (Complex from Human immunodeficiency virus 1)
- Gag-pol polyprotein (24 kDa, Protein from Human immunodeficiency virus 1)
- Peptidyl-prolyl cis-trans isomerase a (17 kDa, Protein from Homo sapiens)
- In vitro assembled hiv-1 capsid in tubular assembly (Complex)
- Cyclophilin a (Complex from Homo sapiens)
Resolution: 6.1 Å
EM Method: Single-particle
Fitted PDBs: 6y9y
Q-score: 0.171
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
- Hiv-1 capsid (Complex from Human immunodeficiency virus 1)
- Gag-pol polyprotein (24 kDa, Protein from Human immunodeficiency virus 1)
- Peptidyl-prolyl cis-trans isomerase a (17 kDa, Protein from Homo sapiens)
- In vitro assembled hiv-1 capsid in tubular assembly (Complex)
- Cyclophilin a (Complex from Homo sapiens)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6y9z
Q-score: 0.203
Ni T, Gerard S, Zhao G, Dent K, Ning J, Zhou J, Shi J, Anderson-Daniels J, Li W, Jang S, Engelman AN, Aiken C, Zhang P
Nat Struct Mol Biol (2020) 27 pp. 855-862 [ Pubmed: 32747784 DOI: doi:10.1038/s41594-020-0467-8 ]
- Hiv-1 capsid (Complex from Human immunodeficiency virus 1)
- Gag-pol polyprotein (24 kDa, Protein from Human immunodeficiency virus 1)
- Peptidyl-prolyl cis-trans isomerase a (17 kDa, Protein from Homo sapiens)
- In vitro assembled hiv-1 capsid in tubular assembly (Complex)
- Cyclophilin a (Complex from Homo sapiens)