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))
CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome
Resolution: 4.67 Å
EM Method: Single-particle
Fitted PDBs: 6u8q
Q-score: 0.176
Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R
J Mol Biol (2020) 432 pp. 2055-2066 [ DOI: doi:10.1016/j.jmb.2020.01.040 Pubmed: 32061936 ]
- Hiv-1 csc intasome (Complex from Human immunodeficiency virus 1)
- Magnesium ion (24 Da, Ligand)
- Integrase (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (27-mer) (8 kDa, DNA from Escherichia coli)
- (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 (25-mer) (7 kDa, DNA from Escherichia coli)
CryoEM structure of HIV-1 conserved Intasome Core
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6vdk
Q-score: 0.281
Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R
J Mol Biol (2020) 432 pp. 2055-2066 [ DOI: doi:10.1016/j.jmb.2020.01.040 Pubmed: 32061936 ]
- Magnesium ion (24 Da, Ligand)
- Hiv-1 conserved intasome core (Complex from Human immunodeficiency virus 1)
- Integrase (39 kDa, Protein from Human immunodeficiency virus 1)
- Dna (27-mer) (8 kDa, DNA from Escherichia coli)
- (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 (25-mer) (7 kDa, DNA from Escherichia coli)