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 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 [ Pubmed: 28059770 DOI: doi:10.1126/science.aah7002 ]
- Intergrase (Complex from Visna/maedi virus EV1 KV1772)
- Vdna, non-transferred strand (6 kDa, DNA from Visna lentivirus (strain 1514))
- Vdna, transferred strand (5 kDa, DNA from Visna-maedi virus)
- Maedi-visna virus (mvv) intasome (542 kDa, Complex)
- Vdna (Complex from Visna-maedi virus)
- Integrase (32 kDa, Protein from Visna/maedi virus EV1 KV1772)
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)
Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ouf
Q-score: 0.431
Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN
Nat Commun (2021) 12 pp. 4996-4996 [ Pubmed: 34404793 DOI: doi:10.1038/s41467-021-25284-1 ]
- Complex of stlv-1 marb43 integrase with nascent viral dna, the human pp2a b56 subunit and the drug inhibitor xz450 (331 kDa, Complex)
- Isoform 3 of pc4 and sfrs1-interacting protein,isoform gamma-1 of serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (80 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Dna (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3') (8 kDa, DNA from Simian T-lymphotropic virus 1)
- 4-azanyl-~{n}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide (445 Da, Ligand)
- Dna (5'-d(*ap*cp*tp*gp*tp*gp*tp*tp*tp*gp*gp*cp*gp*cp*tp*tp*cp*tp*cp*tp*c)-3') (9 kDa, DNA from Simian T-lymphotropic virus 1)
- Zinc ion (65 Da, Ligand)
- Integrase (33 kDa, Protein from Simian T-lymphotropic virus 1)
STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7oug
Q-score: 0.419
Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN
Nat Commun (2021) 12 pp. 4996-4996 [ Pubmed: 34404793 DOI: doi:10.1038/s41467-021-25284-1 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Dna (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3') (8 kDa, DNA from Simian T-lymphotropic virus 1)
- Dna (5'-d(*ap*cp*tp*gp*tp*gp*tp*tp*tp*gp*gp*cp*gp*cp*tp*tp*cp*tp*cp*tp*c)-3') (9 kDa, DNA from Simian T-lymphotropic virus 1)
- Isoform 3 of pc4 and sfrs1-interacting protein,isoform gamma-2 of serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (80 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide (444 Da, Ligand)
- Integrase (33 kDa, Protein from Simian T-lymphotropic virus 1)
- Complex of stlv-1 marb43 integrase with nascent viral dna, the human pp2a b56 subunit and the inhibitor raltegravir (331 kDa, Complex)
Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor bictegravir
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7ouh
Q-score: 0.354
Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN
Nat Commun (2021) 12 pp. 4996-4996 [ Pubmed: 34404793 DOI: doi:10.1038/s41467-021-25284-1 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Dna (5'-d(*gp*ap*gp*ap*gp*ap*ap*gp*cp*gp*cp*cp*ap*ap*ap*cp*ap*cp*a)-3') (8 kDa, DNA from Simian T-lymphotropic virus 1)
- Complex of stlv-1 marb43 integrase with nascent viral dna, the human pp2a b56 subunit and the drug inhibitor bictegravir (331 kDa, Complex)
- Pc4 and sfrs1-interacting protein,serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (Complex from Homo sapiens)
- Dna (5'-d(*ap*cp*tp*gp*tp*gp*tp*tp*tp*gp*gp*cp*gp*cp*tp*tp*cp*tp*cp*tp*c)-3') (9 kDa, DNA from Simian T-lymphotropic virus 1)
- Zinc ion (65 Da, Ligand)
- Dna (Complex from Simian T-lymphotropic virus 1)
- Bictegravir (449 Da, Ligand)
- Integrase (Complex from Simian T-lymphotropic virus 1)
- Pc4 and sfrs1-interacting protein,serine/threonine-protein phosphatase 2a 56 kda regulatory subunit gamma isoform (80 kDa, Protein from Homo sapiens)
- Integrase (33 kDa, Protein from Simian T-lymphotropic virus 1)
Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex
Resolution: 8.2 Å
EM Method: Single-particle
Fitted PDBs: 5m0r
Q-score: 0.098
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 [ Pubmed: 28059770 DOI: doi:10.1126/science.aah7002 ]
- Nucleic acid (Complex from synthetic construct)
- Integrase (32 kDa, Protein from Maedi visna virus (strain KV1772))
- Intergrase (Complex from Maedi visna virus (strain KV1772))
- Vdna-tdna, transferred strand, joined to a model tdna (15 kDa, DNA from Visna lentivirus (strain 1514))
- Mvv strand transfer complex (Complex)
- Vdna, non-transfered strand (6 kDa, DNA from Visna lentivirus (strain 1514))
- Nucleic acid (Complex from Visna lentivirus (strain 1514))
- Tdna (7 kDa, DNA from synthetic construct)
Three-dimensional structure of the core MMTV intasome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 3jca
Q-score: 0.245
Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN
Nature (2016) 530 pp. 358-361 [ Pubmed: 26887496 DOI: doi:10.1038/nature16955 ]
- Mmtv u5 dna end (13 kDa, DNA from Mouse mammary tumor virus)
- Betaretroviral integrase (36 kDa, Protein from Mouse mammary tumor virus)
- Mouse mammary tumor virus intasome complex (194 MDa, Sample)