1WAN
 
 | | DNA DTA TRIPLEX, NMR, 7 STRUCTURES | | Descriptor: | DNA (5'-D(*AP*GP*AP*TP*AP*GP*AP*AP*CP*CP*CP*CP*TP*TP*CP*TP*AP*TP*CP*TP*TP*AP*TP*AP*TP*CP*TP*(D3)P*TP*CP*TP*T)-3') | | Authors: | Wang, E, Koshlap, K.M, Gillespie, P, Dervan, P.B, Feigon, J. | | Deposit date: | 1996-01-14 | | Release date: | 1996-07-11 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Solution structure of a pyrimidine-purine-pyrimidine triplex containing the sequence-specific intercalating non-natural base D3.
J.Mol.Biol., 257, 1996
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365D
 | | STRUCTURAL BASIS FOR G C RECOGNITION IN THE DNA MINOR GROOVE | | Descriptor: | DNA (5'-D(*CP*CP*AP*GP*GP*(CBR)P*CP*TP*GP*G)-3'), IMIDAZOLE-PYRROLE POLYAMIDE | | Authors: | Kielkopf, C.L, Baird, E.E, Dervan, P.B, Rees, D.C. | | Deposit date: | 1997-12-17 | | Release date: | 1998-02-05 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for G.C recognition in the DNA minor groove.
Nat.Struct.Biol., 5, 1998
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1M18
 | | LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA | | Descriptor: | Histone H2A.1, Histone H2B.1, Histone H3.2, ... | | Authors: | Suto, R.K, Edayathumangalam, R.S, White, C.L, Melander, C, Gottesfeld, J.M, Dervan, P.B, Luger, K. | | Deposit date: | 2002-06-18 | | Release date: | 2003-02-18 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands
J.Mol.Biol., 326, 2003
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1M19
 | | LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA | | Descriptor: | 3-AMINO-(DIMETHYLPROPYLAMINE), 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID, 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID, ... | | Authors: | Suto, R.K, Edayathumangalam, R.S, White, C.L, Melander, C, Gottesfeld, J.M, Dervan, P.B, Luger, K. | | Deposit date: | 2002-06-18 | | Release date: | 2003-02-18 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands
J.Mol.Biol., 326, 2003
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8PSH
 | | HIGH RESOLUTION NMR STRUCTURE OF THE STEREOREGULAR (ALL-RP)-PHOSPHOROTHIOATE-DNA/RNA HYBRID D (G*PS*C*PS*G*PS*T*PS*C*PS*A*PS*G*PS*G)R(CCUGACGC), MINIMIZED AVERAGE STRUCTURE | | Descriptor: | DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS)P*(GS)P*(GS))-3'), RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3') | | Authors: | Bachelin, M, Hessler, G, Kurz, G, Hacia, J.G, Dervan, P.B, Kessler, H. | | Deposit date: | 1997-10-13 | | Release date: | 1998-05-27 | | Last modified: | 2022-03-16 | | Method: | SOLUTION NMR | | Cite: | Structure of a Stereoregular Phosphorothioate DNA/RNA Duplex
Nat.Struct.Biol., 5, 1998
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3I5E
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3I5L
 | | Allosteric Modulation of DNA by Small Molecules | | Descriptor: | (22R,51R)-22,51-diamino-5,11,17,28,34,40,46,57-octamethyl-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46,49,54,57,60,61,64,6 5-docosaazanonacyclo[54.2.1.1~4,7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45,48~]hexahexaconta-1(58),4(66),6,10( 65),12,16(64),18,27(63),29,33(62),35,39(61),41,45(60),47,56(59)-hexadecaene-3,9,15,21,26,32,38,44,50,55-decone, 5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3', CALCIUM ION | | Authors: | Chenoweth, D.M, Dervan, P.B. | | Deposit date: | 2009-07-05 | | Release date: | 2009-07-28 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (1.18 Å) | | Cite: | Allosteric modulation of DNA by small molecules
Proc.Natl.Acad.Sci.USA, 106, 2009
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408D
 | | STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA | | Descriptor: | DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'), IMIDAZOLE-PYRROLE POLYAMIDE | | Authors: | Kielkopf, C.L, White, S, Szewczyk, J.W, Turner, J.M, Baird, E.E, Dervan, P.B, Rees, D.C. | | Deposit date: | 1998-06-24 | | Release date: | 1998-10-19 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.
Science, 282, 1998
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8DRH
 | | HIGH RESOLUTION NMR STRUCTURE OF THE D(GCGTCAGG)R(CCUGACGC) HYBRID, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*CP*AP*GP*G)-3'), RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3') | | Authors: | Bachelin, M, Hessler, G, Kurz, G, Hacia, J.G, Dervan, P.B, Kessler, H. | | Deposit date: | 1997-10-13 | | Release date: | 1998-05-27 | | Last modified: | 2022-03-16 | | Method: | SOLUTION NMR | | Cite: | Structure of a Stereoregular Phosphorothioate DNA/RNA Duplex
Nat.Struct.Biol., 5, 1998
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1LEJ
 | | NMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-Im-Py-Beta-Dp) with the Tridecamer DNA Duplex 5'-CCAAAGAGAAGCG-3' | | Descriptor: | 5'-D(*CP*CP*AP*AP*AP*GP*AP*GP*AP*AP*GP*CP*G)-3', 5'-D(*CP*GP*CP*TP*TP*CP*TP*CP*TP*TP*TP*GP*G)-3', IMIDAZOLE-PYRROLE-BETA ALANINE-IMIDAZOLE-BETA ALANINE-IMIDAZOLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE | | Authors: | Urbach, A.R, Love, J.J, Ross, S.A, Dervan, P.B. | | Deposit date: | 2002-04-09 | | Release date: | 2002-05-08 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif.
J.Mol.Biol., 320, 2002
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1PQQ
 | | NMR Structure of a Cyclic Polyamide-DNA Complex | | Descriptor: | 45-(3-AMINOPROPYL)-5,11,22,28,34-PENTAMETHYL-3,9,15,20,26,32,38,43-OCTAOXO-2,5,8,14,19,22,25,28,31,34,37,42,45,48-TETRADECAAZA-11-AZONIAHEPTACYCLO[42.2.1.1~4,7~.1~10,13~.1~21,24~.1~27,30~.1~33,36~]DOPENTACONTA-1(46),4(52),6,10(51),12,21(50),23,27(49),29,33(48),35,44(47)-DODECAENE, 5'-D(*CP*GP*CP*TP*AP*AP*CP*AP*GP*GP*C)-3', 5'-D(*GP*CP*CP*TP*GP*TP*TP*AP*GP*CP*G)-3' | | Authors: | Zhang, Q, Dwyer, T.J, Tsui, V, Case, D.A, Cho, J, Dervan, P.B, Wemmer, D.E. | | Deposit date: | 2003-06-18 | | Release date: | 2004-06-29 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | NMR Structure of a Cyclic Polyamide-DNA Complex.
J.Am.Chem.Soc., 126, 2004
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1M1A
 | | LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA | | Descriptor: | 3-AMINO-(DIMETHYLPROPYLAMINE), 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID, 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID, ... | | Authors: | Suto, R.K, Edayathumangalam, R.S, White, C.L, Melander, C, Gottesfeld, J.M, Dervan, P.B, Luger, K. | | Deposit date: | 2002-06-18 | | Release date: | 2003-02-18 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands
J.MOL.BIOL., 326, 2003
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1S32
 | | Molecular Recognition of the Nucleosomal 'Supergroove' | | Descriptor: | 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE, 3-AMINO-(DIMETHYLPROPYLAMINE), 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID, ... | | Authors: | Edayathumangalam, R.S, Weyermann, P, Gottesfeld, J.M, Dervan, P.B, Luger, K. | | Deposit date: | 2004-01-12 | | Release date: | 2004-05-11 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Molecular Recognition of the Nucleosomal 'Supergroove'
Proc.Natl.Acad.Sci.USA, 101, 2004
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1CVY
 | | CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG | | Descriptor: | 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3', IMIDAZOLE-PYRROLE POLYAMIDE | | Authors: | Kielkopf, C.L, Bremer, R.E, White, S, Baird, E.E, Dervan, P.B, Rees, D.C. | | Deposit date: | 1999-08-24 | | Release date: | 2000-01-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
J.Mol.Biol., 295, 2000
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1CVX
 | | CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG | | Descriptor: | 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3', HYDROXYPYRROLE-IMIDAZOLE-PYRROLE POLYAMIDE | | Authors: | Kielkopf, C.L, Bremer, R.E, White, S, Baird, E.E, Dervan, P.B, Rees, D.C. | | Deposit date: | 1999-08-24 | | Release date: | 2000-01-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.27 Å) | | Cite: | Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
J.Mol.Biol., 295, 2000
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7RIX
 | | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 2 | | Descriptor: | 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIW
 | | RNA polymerase II elongation complex scaffold 2, without polyamide | | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIL
 | | Crystal structure of hairpin polyamide Py-Im 1 bound to 5' CCTGACCAGG | | Descriptor: | 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid, ACETATE ION, non-template DNA, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIY
 | | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 2 soaked with UTP | | Descriptor: | 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIM
 | | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 | | Descriptor: | 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIP
 | | RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 soaked with CTP | | Descriptor: | 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7RIQ
 | | RNA polymerase II elongation complex scaffold 1 without polyamide | | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | | Authors: | Oh, J, Dervan, P.B, Wang, D. | | Deposit date: | 2021-07-20 | | Release date: | 2022-01-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Proc.Natl.Acad.Sci.USA, 119, 2022
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3OMJ
 | | Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding | | Descriptor: | (23R,52R)-23,52-diamino-5,11,17,28,34,40,46,57-octamethyl-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46,49,54,57,60,64-icosaazanonacyclo[54.2.1.1~4,7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45,48~]hexahexaconta-1(58),4(66),6,10(65),12,16(64),18,27(63),29,33(62),35,39(61),41,45(60),47,56(59)-hexadecaene-3,9,15,21,26,32,38,44,50,55-decone, 5'-D(*CP*(C38)P*AP*GP*TP*AP*CP*TP*GP*G)-3', CALCIUM ION | | Authors: | Chenoweth, D.M. | | Deposit date: | 2010-08-27 | | Release date: | 2010-09-08 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (0.95 Å) | | Cite: | Structural basis for cyclic py-im polyamide allosteric inhibition of nuclear receptor binding.
J.Am.Chem.Soc., 132, 2010
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1GN7
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5VVS
 | | RNA pol II elongation complex | | Descriptor: | DNA (NTS), DNA (TS), DNA-directed RNA polymerase II subunit RPB1, ... | | Authors: | Lahiri, I, Leschziner, A.E. | | Deposit date: | 2017-05-20 | | Release date: | 2017-11-22 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (6.4 Å) | | Cite: | Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
Nature, 551, 2017
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