3VRH
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![BU of 3vrh by Molmil](/molmil-images/mine/3vrh) | Crystal structure of ph0300 | Descriptor: | BICINE, Putative uncharacterized protein PH0300, ZINC ION | Authors: | Nakagawa, H, Kuratani, M, Goto-Ito, S, Ito, T, Sekine, S.I, Yokoyama, S. | Deposit date: | 2012-04-10 | Release date: | 2013-03-13 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Proteins, 2013
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2CYA
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![BU of 2cya by Molmil](/molmil-images/mine/2cya) | Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix | Descriptor: | SULFATE ION, Tyrosyl-tRNA synthetase | Authors: | Kuratani, M, Sakai, H, Takahashi, M, Yanagisawa, T, Kobayashi, T, Murayama, K, Chen, L, Liu, Z.J, Wang, B.C, Kuroishi, C, Kuramitsu, S, Terada, T, Bessho, Y, Shirouzu, M, Sekine, S.I, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-07-06 | Release date: | 2005-11-22 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea J.Mol.Biol., 355, 2005
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5ZAB
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![BU of 5zab by Molmil](/molmil-images/mine/5zab) | Crystal structure of cf3-aequorin | Descriptor: | (2S)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-{[4-(trifluoromethyl)phenyl]methyl}imidazo[1,2-a]pyrazin-3(2H)-one, Aequorin-2 | Authors: | Inouye, S, Tomabechi, Y, Sekine, S.I, Shirouzu, M, Hosoya, T. | Deposit date: | 2018-02-07 | Release date: | 2018-06-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.147 Å) | Cite: | Slow luminescence kinetics of semi-synthetic aequorin: expression, purification and structure determination of cf3-aequorin. J. Biochem., 164, 2018
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4WQT
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![BU of 4wqt by Molmil](/molmil-images/mine/4wqt) | Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GreA/Gfh1 chimeric protein) | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | Authors: | Murayama, Y, Sekine, S, Yokoyama, S. | Deposit date: | 2014-10-22 | Release date: | 2015-02-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (4.4 Å) | Cite: | The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions. Mol.Cell, 57, 2015
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4WQS
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![BU of 4wqs by Molmil](/molmil-images/mine/4wqs) | Thermus thermophilus RNA polymerase backtracked complex | Descriptor: | DNA (28-MER), DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3'), DNA-directed RNA polymerase subunit alpha, ... | Authors: | Murayama, Y, Sekine, S, Yokoyama, S. | Deposit date: | 2014-10-22 | Release date: | 2015-02-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (4.306 Å) | Cite: | The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions. Mol.Cell, 57, 2015
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2ZOD
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![BU of 2zod by Molmil](/molmil-images/mine/2zod) | Crystal structure of selenophosphate synthetase from Aquifex aeolicus | Descriptor: | SULFATE ION, Selenide, water dikinase | Authors: | Sekine, S.I, Matsumoto, E, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2008-05-09 | Release date: | 2008-05-27 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs. J.Mol.Biol., 385, 2009
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7XT7
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![BU of 7xt7 by Molmil](/molmil-images/mine/7xt7) | RNA polymerase II elongation complex transcribing a nucleosome (EC49B) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-16 | Release date: | 2022-10-12 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (4.2 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7XTI
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![BU of 7xti by Molmil](/molmil-images/mine/7xti) | RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-17 | Release date: | 2022-10-12 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7YQ8
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![BU of 7yq8 by Molmil](/molmil-images/mine/7yq8) | Cryo-EM structure of human topoisomerase II beta in complex with DNA and etoposide | Descriptor: | (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, 50-mer DNA, DNA topoisomerase 2-beta, ... | Authors: | Naganuma, M, Ehara, H, Kim, D, Nakagawa, R, Cong, A, Bu, H, Jeong, J, Jang, J, Schellenberg, M.J, Bunch, H, Sekine, S. | Deposit date: | 2022-08-05 | Release date: | 2024-01-03 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes. Nat Commun, 14, 2023
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6A5U
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![BU of 6a5u by Molmil](/molmil-images/mine/6a5u) | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation | Descriptor: | DNA (198-MER), DNA (40-MER), DNA-directed RNA polymerase subunit, ... | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | Deposit date: | 2018-06-25 | Release date: | 2018-10-03 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (7.6 Å) | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage. Science, 362, 2018
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6A5P
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![BU of 6a5p by Molmil](/molmil-images/mine/6a5p) | RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | Deposit date: | 2018-06-25 | Release date: | 2018-10-03 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (7 Å) | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage. Science, 362, 2018
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6A5O
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![BU of 6a5o by Molmil](/molmil-images/mine/6a5o) | RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | Deposit date: | 2018-06-25 | Release date: | 2018-10-03 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (9.9 Å) | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage. Science, 362, 2018
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8KB5
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![BU of 8kb5 by Molmil](/molmil-images/mine/8kb5) | Cryo-EM structure of the human nucleosome containing H3.8 | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Hirai, H, Kujirai, T, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-08-03 | Release date: | 2023-10-18 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.26133 Å) | Cite: | Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8. J.Biochem., 174, 2023
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8YBK
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![BU of 8ybk by Molmil](/molmil-images/mine/8ybk) | Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kimura, T, Hirai, S, Kujirai, T, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2024-02-14 | Release date: | 2024-07-24 | Method: | ELECTRON MICROSCOPY (2.69 Å) | Cite: | Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K. Genes Cells, 2024
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8YBJ
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![BU of 8ybj by Molmil](/molmil-images/mine/8ybj) | Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Kimura, T, Hirai, S, Kujirai, T, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2024-02-14 | Release date: | 2024-07-24 | Method: | ELECTRON MICROSCOPY (2.38 Å) | Cite: | Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K. Genes Cells, 2024
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5B0U
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![BU of 5b0u by Molmil](/molmil-images/mine/5b0u) | |
7XN7
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![BU of 7xn7 by Molmil](/molmil-images/mine/7xn7) | RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C | Descriptor: | Chromatin elongation factor SPT5, Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-04-28 | Release date: | 2022-09-07 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.1 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7XSE
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![BU of 7xse by Molmil](/molmil-images/mine/7xse) | RNA polymerase II elongation complex transcribing a nucleosome (EC42) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-13 | Release date: | 2022-09-07 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7XSX
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![BU of 7xsx by Molmil](/molmil-images/mine/7xsx) | RNA polymerase II elongation complex transcribing a nucleosome (EC49) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-15 | Release date: | 2022-09-07 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7XTD
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![BU of 7xtd by Molmil](/molmil-images/mine/7xtd) | RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-16 | Release date: | 2022-09-07 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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7XSZ
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![BU of 7xsz by Molmil](/molmil-images/mine/7xsz) | RNA polymerase II elongation complex transcribing a nucleosome (EC115) | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | Deposit date: | 2022-05-15 | Release date: | 2022-09-07 | Last modified: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science, 377, 2022
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3AOH
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![BU of 3aoh by Molmil](/molmil-images/mine/3aoh) | RNA polymerase-Gfh1 complex (Crystal type 1) | Descriptor: | Anti-cleavage anti-GreA transcription factor Gfh1, DNA (5'-D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*AP*CP*CP*GP*CP*CP*GP*CP*AP*T)-3'), DNA-directed RNA polymerase subunit alpha, ... | Authors: | Tagami, S, Sekine, S, Kumarevel, T, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2010-09-28 | Release date: | 2010-12-08 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (4.1 Å) | Cite: | Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein Nature, 468, 2010
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3AOI
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![BU of 3aoi by Molmil](/molmil-images/mine/3aoi) | RNA polymerase-Gfh1 complex (Crystal type 2) | Descriptor: | Anti-cleavage anti-GreA transcription factor Gfh1, DNA (5'-D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*CP*GP*CP*AP*T)-3'), DNA-directed RNA polymerase subunit alpha, ... | Authors: | Tagami, S, Sekine, S, Kumarevel, T, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2010-09-30 | Release date: | 2010-12-08 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (4.3 Å) | Cite: | Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein Nature, 468, 2010
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7VSX
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![BU of 7vsx by Molmil](/molmil-images/mine/7vsx) | Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L18Q and V27L) | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, QLnK | Authors: | Tomabechi, Y, Sekine, S, Shirouzu, M, Takamitsu, H, Satoshi, I. | Deposit date: | 2021-10-27 | Release date: | 2022-08-24 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.698 Å) | Cite: | Reverse mutants of the catalytic 19 kDa mutant protein (nanoKAZ/nanoLuc) from Oplophorus luciferase with coelenterazine as preferred substrate. Plos One, 17, 2022
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7WBX
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![BU of 7wbx by Molmil](/molmil-images/mine/7wbx) | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Osumi, K, Kujirai, T, Ehara, H, Sekine, S, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2021-12-17 | Release date: | 2023-07-05 | Last modified: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome. J.Mol.Biol., 435, 2023
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