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)
Wei G, Iqbal N, Courouble VV, Francis AC, Singh PK, Hudait A, Annamalai AS, Bester S, Huang SW, Shkriabai N, Briganti L, Haney R, KewalRamani VN, Voth GA, Engelman AN, Melikyan GB, Griffin PR, Asturias F, Kvaratskhelia M
Nat Commun (2022) 13 pp. 5879-5879 [ Pubmed: 36202818 DOI: doi:10.1038/s41467-022-33662-6 ]
Wei G, Iqbal N, Courouble VV, Francis AC, Singh PK, Hudait A, Annamalai AS, Bester S, Huang SW, Shkriabai N, Briganti L, Haney R, KewalRamani VN, Voth GA, Engelman AN, Melikyan GB, Griffin PR, Asturias F, Kvaratskhelia M
Nat Commun (2022) 13 pp. 5879-5879 [ DOI: doi:10.1038/s41467-022-33662-6 Pubmed: 36202818 ]
Wei G, Iqbal N, Courouble VV, Francis AC, Singh PK, Hudait A, Annamalai AS, Bester S, Huang SW, Shkriabai N, Briganti L, Haney R, KewalRamani VN, Voth GA, Engelman AN, Melikyan GB, Griffin PR, Asturias F, Kvaratskhelia M
Nat Commun (2022) 13 pp. 5879-5879 [ DOI: doi:10.1038/s41467-022-33662-6 Pubmed: 36202818 ]
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 ]
- Vdna strand (non-transferred) (9 kDa, DNA from Mouse mammary tumor virus)
- Integrase (35 kDa, Protein from Mouse mammary tumor virus)
- Calcium ion (40 Da, Ligand)
- Mmtv strand transfer complex intasome (300 kDa, Complex from Mouse mammary tumor virus)
- Tdna strand (4 kDa, DNA from Mouse mammary tumor virus)
- Vdna-tdna strand (transferred) (12 kDa, DNA from Mouse mammary tumor virus)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1093/nar/gkac644 Pubmed: 35947647 ]
- Integrase (35 kDa, Protein from Mouse mammary tumor virus)
- Higher-order assembly of multiple mmtv strand transfer complex intasomes (600 kDa, Complex from Mouse mammary tumor virus)
- Tdna strand (4 kDa, DNA from Mouse mammary tumor virus)
- Vdna-tdna strand (transferred) (12 kDa, DNA from Mouse mammary tumor virus)
- Vdna strand (non-transferred) (6 kDa, DNA from Mouse mammary tumor virus)
- Zinc ion (65 Da, Ligand)
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 ]
- 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)
- Pol polyprotein (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Dna (5'-d(p*tp*tp*gp*ap*tp*tp*ap*gp*gp*gp*tp*g)-3') (7 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)
- Dna (37-mer) (15 kDa, DNA from DNA molecule)
MVV cleaved synaptic complex (CSC) intasome at 4.5 A resolution (re-refined)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7zpp
Q-score: 0.097
Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jonsson SR, Kotecha A, Cook NJ, Pye VE, Taylor IA, Andresdottir V, Engelman AN, Costa A, Cherepanov P
Science (2017) 355 pp. 93-95 [ DOI: doi:10.1126/science.aah7002 Pubmed: 28059770 ]
- Intergrase (Complex from Visna/maedi virus EV1 KV1772)
- Vdna, non-transferred strand (6 kDa, DNA from Visna lentivirus (strain 1514))
- Integrase (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Vdna, transferred strand (5 kDa, DNA from Visna-maedi virus)
- Vdna (Complex from Visna-maedi virus)
- Maedi-visna virus (mvv) intasome (542 kDa, Complex)
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 ]
- Mvv cleaved synaptic complex intasome (480 kDa, Complex from Streptomyces griseus)
- Dna ev272 (8 kDa, DNA from synthetic construct)
- Calcium ion (40 Da, Ligand)
- Integrase (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
- Dna ev273 (8 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
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 [ DOI: doi:10.1038/s42003-021-01855-2 Pubmed: 33712691 ]
- Integrase (30 kDa, Protein from Rous sarcoma virus (strain Schmidt-Ruppin A))
- Magnesium ion (24 Da, Ligand)
- 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)
- 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))
- Zinc ion (65 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))