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4C3G
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BU of 4c3g by Molmil
cryo-EM structure of activated and oligomeric restriction endonuclease SgrAI
Descriptor: 5'-D(*CP*CP*GP*GP*TP*GP*TP*GP*AP*AP*GP*AP*CP*CP *CP*AP*CP*GP*CP*AP*TP*CP)-3', 5'-D(*GP*AP*TP*GP*CP*GP*TP*GP*GP*GP*TP*CP*TP*TP *CP*AP*CP*AP)-3', SGRAIR RESTRICTION ENZYME
Authors:Lyumkis, D, Talley, H, Stewart, A, Shah, S, Park, C.K, Tama, F, Potter, C.S, Carragher, B, Horton, N.C.
Deposit date:2013-08-23
Release date:2013-09-11
Last modified:2017-08-23
Method:ELECTRON MICROSCOPY (8.6 Å)
Cite:Allosteric Regulation of DNA Cleavage and Sequence-Specificity Through Run-on Oligomerization.
Structure, 21, 2013
3J5M
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BU of 3j5m by Molmil
Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs
Descriptor: BG505 SOSIP gp120, BG505 SOSIP gp41, PGV04 heavy chain, ...
Authors:Lyumkis, D, Julien, J.-P, Wilson, I.A, Ward, A.B.
Deposit date:2013-10-26
Release date:2013-11-13
Last modified:2018-07-18
Method:ELECTRON MICROSCOPY (5.8 Å)
Cite:Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.
Science, 342, 2013
6V3K
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BU of 6v3k by Molmil
Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ419 (compound 4c)
Descriptor: 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-(5-oxidanylpentyl)-1,8-naphthyridine-3-carboxamide, Chimeric Sso7d and HIV-1 integrase, MAGNESIUM ION, ...
Authors:Lyumkis, D, Jozwik, I.K, Passos, D.
Deposit date:2019-11-25
Release date:2020-02-12
Last modified:2024-03-06
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Science, 367, 2020
6PUW
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BU of 6puw by Molmil
Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and Bictegravir (BIC)
Descriptor: Bictegravir, Chimeric Sso7d and HIV-1 integrase, MAGNESIUM ION, ...
Authors:Lyumkis, D, Jozwik, I.K, Passos, D.
Deposit date:2019-07-18
Release date:2020-02-12
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Science, 367, 2020
6PUZ
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BU of 6puz by Molmil
Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f)
Descriptor: 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide, Chimeric Sso7d and HIV-1 integrase, MAGNESIUM ION, ...
Authors:Lyumkis, D, Jozwik, I.K, Passos, D.
Deposit date:2019-07-18
Release date:2020-02-12
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Science, 367, 2020
6PUY
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BU of 6puy by Molmil
Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ426 (compound 4d)
Descriptor: 4-amino-N-[(2,4-difluorophenyl)methyl]-1-hydroxy-6-(6-hydroxyhexyl)-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamide, Chimeric Sso7d and HIV-1 integrase, MAGNESIUM ION, ...
Authors:Lyumkis, D, Jozwik, I.K, Passos, D.
Deposit date:2019-07-18
Release date:2020-02-12
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Science, 367, 2020
7SEP
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BU of 7sep by Molmil
Cryo-EM Structure of the RT component of the HIV-1 Pol Polyprotein
Descriptor: Gag-Pol polyprotein
Authors:Lyumkis, D, Passos, D, Arnold, E, Harrison, J.J.E.
Deposit date:2021-10-01
Release date:2022-07-27
Last modified:2022-08-03
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation.
Sci Adv, 8, 2022
6PUT
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BU of 6put by Molmil
Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium
Descriptor: CALCIUM ION, Chimeric Sso7d and HIV-1 integrase, ZINC ION, ...
Authors:Lyumkis, D, Jozwik, I.K, Passos, D.
Deposit date:2019-07-18
Release date:2020-02-12
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Science, 367, 2020
7SJX
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BU of 7sjx by Molmil
Cryo-EM Structure of the PR-RT components of the HIV-1 Pol Polyprotein
Descriptor: Gag-Pol polyprotein
Authors:Lyumkis, D, Passos, D, Arnold, E, Harrison, J.J.E.K, Ruiz, F.X.
Deposit date:2021-10-19
Release date:2022-07-27
Last modified:2023-08-16
Method:ELECTRON MICROSCOPY (8.2 Å)
Cite:Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation.
Sci Adv, 8, 2022
5TQX
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BU of 5tqx by Molmil
CryoEM reconstruction of human IKK1, intermediate conformation 2
Descriptor: Inhibitor of nuclear factor kappa-B kinase subunit alpha
Authors:Lyumkis, D, Ghosh, G, Polley, S, Biswath, T, Huang, D, Passos, D.O.
Deposit date:2016-10-24
Release date:2016-11-09
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (5.4 Å)
Cite:Structural Basis for the Activation of IKK1/ alpha.
Cell Rep, 17, 2016
5TQW
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BU of 5tqw by Molmil
CryoEM reconstruction of human IKK1, open conformation 1
Descriptor: Inhibitor of nuclear factor kappa-B kinase subunit alpha
Authors:Lyumkis, D, Ghosh, G, Polley, S, Biswath, T, Huang, D, Passos, D.O.
Deposit date:2016-10-24
Release date:2016-11-09
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (5.6 Å)
Cite:Structural Basis for the Activation of IKK1/ alpha.
Cell Rep, 17, 2016
5TQY
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BU of 5tqy by Molmil
CryoEM reconstruction of human IKK1, closed conformation 3
Descriptor: Inhibitor of nuclear factor kappa-B kinase subunit alpha
Authors:Lyumkis, D, Ghosh, G, Polley, S, Biswath, T, Huang, D, Passos, D.O.
Deposit date:2016-10-24
Release date:2016-11-09
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (5.2 Å)
Cite:Structural Basis for the Activation of IKK1/ alpha.
Cell Rep, 17, 2016
5U1C
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BU of 5u1c by Molmil
Structure of tetrameric HIV-1 Strand Transfer Complex Intasome
Descriptor: DNA (11-MER), DNA (23-MER), DNA (37-MER), ...
Authors:Lyumkis, D, Passos, D.
Deposit date:2016-11-28
Release date:2017-01-11
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.
Science, 355, 2017
8SY6
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BU of 8sy6 by Molmil
E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site
Descriptor: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ...
Authors:Shan, Z, Lyumkis, D, Oh, J, Wang, D.
Deposit date:2023-05-24
Release date:2023-12-27
Method:ELECTRON MICROSCOPY (3.28 Å)
Cite:A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
8SY7
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BU of 8sy7 by Molmil
E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-STP base pair in the active site
Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ...
Authors:Shan, Z, Lyumkis, D, Oh, J, Wang, D.
Deposit date:2023-05-24
Release date:2023-12-27
Method:ELECTRON MICROSCOPY (2.65 Å)
Cite:A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
8SY5
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BU of 8sy5 by Molmil
E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site
Descriptor: 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ...
Authors:Shan, Z, Lyumkis, D, Oh, J, Wang, D.
Deposit date:2023-05-24
Release date:2023-12-27
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
8TXO
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BU of 8txo by Molmil
E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dZ-PTP base pair in the active site
Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ...
Authors:Aiyer, S, Shan, Z, Oh, J, Wang, D, Tan, Y.Z, Lyumkis, D.
Deposit date:2023-08-23
Release date:2024-01-24
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Overcoming resolution attenuation during tilted cryo-EM data collection.
Nat Commun, 15, 2024
4NCO
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BU of 4nco by Molmil
Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, BG505 SOSIP gp120, BG505 SOSIP gp41, ...
Authors:Julien, J.-P, Stanfield, R.L, Lyumkis, D, Ward, A.B, Wilson, I.A.
Deposit date:2013-10-24
Release date:2013-11-13
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (4.7 Å)
Cite:Crystal structure of a soluble cleaved HIV-1 envelope trimer.
Science, 342, 2013
7USF
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BU of 7usf by Molmil
Mouse mammary tumor virus strand transfer complex intasome
Descriptor: CALCIUM ION, Integrase, ZINC ION, ...
Authors:Jozwik, I, Lyumkis, D.
Deposit date:2022-04-25
Release date:2022-08-24
Last modified:2022-11-23
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:B-to-A transition in target DNA during retroviral integration.
Nucleic Acids Res., 50, 2022
7UT1
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BU of 7ut1 by Molmil
Higher-order assembly of multiple MMTV strand transfer complex intasomes
Descriptor: Integrase, ZINC ION, tDNA strand, ...
Authors:Jozwik, I, Lyumkis, D.
Deposit date:2022-04-26
Release date:2022-08-24
Last modified:2022-11-23
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:B-to-A transition in target DNA during retroviral integration.
Nucleic Acids Res., 50, 2022
5EBZ
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BU of 5ebz by Molmil
Crystal structure of human IKK1
Descriptor: 2,3-di-O-sulfo-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-2,4-di-O-sulfo-alpha-D-glucopyranose, 2-azanyl-5-phenyl-3-(4-sulfamoylphenyl)benzamide, Inhibitor of nuclear factor kappa-B kinase subunit alpha, ...
Authors:Polley, S, Passos, D, Huang, D, Biswas, T, Verma, I, Lyumkis, D, Ghosh, G.
Deposit date:2015-10-20
Release date:2016-11-02
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (4.5 Å)
Cite:Structural Basis for the Activation of IKK1/ alpha.
Cell Rep, 17, 2016
6ME0
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BU of 6me0 by Molmil
Structure of a group II intron retroelement prior to DNA integration
Descriptor: MAGNESIUM ION, Maturase reverse transcriptase, SODIUM ION, ...
Authors:Haack, D, Yan, X, Zhang, C, Hingey, J, Lyumkis, D, Baker, T.S, Toor, N.
Deposit date:2018-09-05
Release date:2019-08-14
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.
Cell, 178, 2019
6MEC
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BU of 6mec by Molmil
Structure of a group II intron retroelement after DNA integration
Descriptor: MAGNESIUM ION, Maturase reverse transcriptase, SODIUM ION, ...
Authors:Haack, D, Yan, X, Zhang, C, Hingey, J, Lyumkis, D, Baker, T.S, Toor, N.
Deposit date:2018-09-06
Release date:2019-08-14
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.
Cell, 178, 2019
7SS5
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BU of 7ss5 by Molmil
Activated SgrAI endonuclease DNA-bound dimer with Ca2+ and intact primary site DNA
Descriptor: CALCIUM ION, DNA (5'-D(P*GP*GP*TP*CP*TP*TP*CP*AP*CP*AP*CP*CP*GP*GP*TP*GP*TP*GP*AP*AP*GP*AP*CP*C)-3'), SgraIR restriction enzyme
Authors:Shan, Z, Lyumkis, D, Horton, N.C.
Deposit date:2021-11-09
Release date:2021-12-01
Last modified:2022-06-15
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity.
J.Biol.Chem., 298, 2022
7U32
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BU of 7u32 by Molmil
MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution
Descriptor: CALCIUM ION, DNA EV272, DNA EV273, ...
Authors:Shan, Z, Pye, V.E, Cherepanov, P, Lyumkis, D.
Deposit date:2022-02-25
Release date:2022-05-11
Last modified:2024-02-21
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Multivalent interactions essential for lentiviral integrase function.
Nat Commun, 13, 2022

 

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