Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
4X67
DownloadVisualize
BU of 4x67 by Molmil
Crystal structure of elongating yeast RNA polymerase II stalled at oxidative Cyclopurine DNA lesions.
Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ...
Authors:Wang, L, Chong, J, Wang, D.
Deposit date:2014-12-07
Release date:2015-02-04
Last modified:2019-12-25
Method:X-RAY DIFFRACTION (4.1 Å)
Cite:Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
Proc.Natl.Acad.Sci.USA, 112, 2015
4Y52
DownloadVisualize
BU of 4y52 by Molmil
Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.
Descriptor: DNA (29-MER), DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, ...
Authors:Wang, L, Chong, J, Wang, D.
Deposit date:2015-02-11
Release date:2015-07-15
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Nature, 523, 2015
4X6A
DownloadVisualize
BU of 4x6a by Molmil
Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions
Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ...
Authors:Wang, L, Chong, J, Wang, D.
Deposit date:2014-12-07
Release date:2015-02-04
Last modified:2019-12-25
Method:X-RAY DIFFRACTION (3.96 Å)
Cite:Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
Proc.Natl.Acad.Sci.USA, 112, 2015
4Y7N
DownloadVisualize
BU of 4y7n by Molmil
The Structure Insight into 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.
Descriptor: DNA (29-MER), DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, ...
Authors:Wang, L, Chong, J, Wang, D.
Deposit date:2015-02-15
Release date:2015-07-15
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Nature, 523, 2015
5VVS
DownloadVisualize
BU of 5vvs by Molmil
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
7RIX
DownloadVisualize
BU of 7rix by Molmil
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
7RIW
DownloadVisualize
BU of 7riw by Molmil
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
7RIL
DownloadVisualize
BU of 7ril by Molmil
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
7RIY
DownloadVisualize
BU of 7riy by Molmil
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
7RIM
DownloadVisualize
BU of 7rim by Molmil
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
7RIP
DownloadVisualize
BU of 7rip by Molmil
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
7RIQ
DownloadVisualize
BU of 7riq by Molmil
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
5W4U
DownloadVisualize
BU of 5w4u by Molmil
Pol II elongation complex with an N6-methyladenine-containing template
Descriptor: 14mer non-template DNA, 29mer template DNA, 9mer RNA, ...
Authors:Wang, W, Wang, D.
Deposit date:2017-06-13
Release date:2018-06-20
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
J.Am.Chem.Soc., 139, 2017
5W51
DownloadVisualize
BU of 5w51 by Molmil
Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP
Descriptor: 14mer non-template DNA, 29mer template DNA, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine, ...
Authors:Wang, W, Wang, D.
Deposit date:2017-06-13
Release date:2018-06-20
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (3.404 Å)
Cite:Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
J.Am.Chem.Soc., 139, 2017
7KED
DownloadVisualize
BU of 7ked by Molmil
RNA polymerase II elongation complex with unnatural base dTPT3
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, Wang, W, Wang, D.
Deposit date:2020-10-10
Release date:2021-06-23
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
Nat.Chem.Biol., 17, 2021
7KEF
DownloadVisualize
BU of 7kef by Molmil
RNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state
Descriptor: (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ...
Authors:Oh, J, Wang, D.
Deposit date:2020-10-10
Release date:2021-06-23
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.89 Å)
Cite:Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
Nat.Chem.Biol., 17, 2021
7KEE
DownloadVisualize
BU of 7kee by Molmil
RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site
Descriptor: (1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ...
Authors:Oh, J, Wang, D.
Deposit date:2020-10-10
Release date:2021-06-23
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.45 Å)
Cite:Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
Nat.Chem.Biol., 17, 2021
8DH4
DownloadVisualize
BU of 8dh4 by Molmil
T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair
Descriptor: (7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine, MAGNESIUM ION, Non-template strand DNA, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
8DH3
DownloadVisualize
BU of 8dh3 by Molmil
T7 RNA polymerase elongation complex with unnatural base dPa
Descriptor: Non-template strand DNA, RNA, T7 RNA polymerase, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
8DH1
DownloadVisualize
BU of 8dh1 by Molmil
T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair
Descriptor: 1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-pyrrole-2-carbaldehyde, GLYCEROL, MAGNESIUM ION, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
8DH0
DownloadVisualize
BU of 8dh0 by Molmil
T7 RNA polymerase elongation complex with unnatural base dDs
Descriptor: GLYCEROL, Non-template strand DNA, RNA, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
8DH5
DownloadVisualize
BU of 8dh5 by Molmil
T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch
Descriptor: ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Non-template strand DNA, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
8DH2
DownloadVisualize
BU of 8dh2 by Molmil
T7 RNA polymerase elongation complex with unnatural base dDs-ATP mismatch
Descriptor: GLYCEROL, MAGNESIUM ION, Non-template strand DNA, ...
Authors:Oh, J, Wang, D.
Deposit date:2022-06-24
Release date:2023-02-01
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Nat Commun, 14, 2023
6UPZ
DownloadVisualize
BU of 6upz by Molmil
RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3
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, Wang, D.
Deposit date:2019-10-18
Release date:2020-06-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
Proc.Natl.Acad.Sci.USA, 117, 2020
6UPY
DownloadVisualize
BU of 6upy by Molmil
RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E
Descriptor: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ...
Authors:Oh, J, Wang, D.
Deposit date:2019-10-18
Release date:2020-06-10
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
Proc.Natl.Acad.Sci.USA, 117, 2020

 

12>

223166

数据于2024-07-31公开中

PDB statisticsPDBj update infoContact PDBjnumon