7MKO
 
 | | Escherichia coli RNA polymerase elongation complex | | Descriptor: | 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (29-MER), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Qayyum, M.Z, Murakami, K.S. | | Deposit date: | 2021-04-26 | | Release date: | 2021-06-02 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.15 Å) | | Cite: | Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
J.Biol.Chem., 297, 2021
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7MKN
 | | Escherichia coli RNA polymerase and RapA elongation complex | | Descriptor: | 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, DNA (29-MER), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Qayyum, M.Z, Murakami, K.S. | | Deposit date: | 2021-04-26 | | Release date: | 2021-06-02 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
J.Biol.Chem., 297, 2021
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7MKQ
 | | Escherichia coli RNA polymerase and RapA binary complex | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Qayyum, M.Z, Murakami, K.S. | | Deposit date: | 2021-04-26 | | Release date: | 2021-06-02 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (4.8 Å) | | Cite: | Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
J.Biol.Chem., 297, 2021
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7MKP
 | | Escherichia coli RNA polymerase core enzyme | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Qayyum, M.Z, Murakami, K.S. | | Deposit date: | 2021-04-26 | | Release date: | 2021-06-23 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.41 Å) | | Cite: | Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
J.Biol.Chem., 297, 2021
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5NWT
 | | Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Zhang, X, Buck, M, Darbari, V.C, Yang, Y, Zhang, N, Lu, D, Glyde, R, Wang, Y, Winkelman, J, Gourse, R.L, Murakami, K.S. | | Deposit date: | 2017-05-08 | | Release date: | 2017-09-13 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (3.76 Å) | | Cite: | TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 reveal new and conserved regulatory strategies.
Science, 349, 2015
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7ML0
 | | RNA polymerase II pre-initiation complex (PIC1) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MEI
 | | Composite structure of EC+EC | | Descriptor: | DNA (74-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-06 | | Release date: | 2022-03-02 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MKA
 | | Structure of EC+EC (leading EC-focused) | | Descriptor: | DNA (40-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-22 | | Release date: | 2022-04-27 | | Last modified: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MK9
 | | Complex structure of trailing EC of EC+EC (trailing EC-focused) | | Descriptor: | DNA (40-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-22 | | Release date: | 2022-04-27 | | Last modified: | 2023-05-17 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML1
 | | RNA polymerase II pre-initiation complex (PIC2) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML3
 | | General transcription factor TFIIH (weak binding) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (7.6 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML4
 | | RNA polymerase II initially transcribing complex (ITC) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-03-09 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML2
 | | RNA polymerase II pre-initiation complex (PIC3) | | Descriptor: | BJ4_G0004860.mRNA.1.CDS.1, BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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3C2P
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8UOQ
 | | Composite map of PIC_delta_TFIIK form2 | | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2023-10-20 | | Release date: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.
Nucleic Acids Res., 2024
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3C3L
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8UOT
 | | Composite map of PICdeltaTFIIK form1 | | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2023-10-20 | | Release date: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.
Nucleic Acids Res., 2024
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8UMH
 | | Consensus map of PICdeltaTFIIK form2 | | Descriptor: | DNA (63-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2023-10-17 | | Release date: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | consensus map of PICdeltaTFIIK form2
To be published
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8UMI
 | | consensus map of PICdeltaTFIIK form1 | | Descriptor: | DNA (64-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2023-10-17 | | Release date: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | consensus map of PICdeltaTFIIK form1
To be published
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6KF4
 | | Cryo-EM structure of Thermococcus kodakarensis RNA polymerase | | Descriptor: | DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit A'', DNA-directed RNA polymerase subunit D, ... | | Authors: | Jun, S.-H, Hyun, J, Jeong, H, Cha, J.S, Kim, H, Bartlett, M.S, Cho, H.-S, Murakami, K.S. | | Deposit date: | 2019-07-06 | | Release date: | 2020-07-01 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.97 Å) | | Cite: | Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase.
Nat Commun, 11, 2020
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6KF3
 | | Cryo-EM structure of Thermococcus kodakarensis RNA polymerase | | Descriptor: | DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit A'', DNA-directed RNA polymerase subunit D, ... | | Authors: | Jun, S.-H, Hyun, J, Jeong, H, Cha, J.S, Kim, H, Bartlett, M.S, Cho, H.-S, Murakami, K.S. | | Deposit date: | 2019-07-06 | | Release date: | 2020-07-01 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase.
Nat Commun, 11, 2020
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6KF9
 | | Cryo-EM structure of Thermococcus kodakarensis RNA polymerase | | Descriptor: | DNA (27-MER), DNA (5'-D(P*TP*CP*GP*GP*TP*AP*AP*TP*CP*AP*CP*GP*CP*TP*CP*C)-3'), DNA-directed RNA polymerase subunit, ... | | Authors: | Jun, S.-H, Hyun, J, Jeong, H, Cha, J.S, Kim, H, Bartlett, M.S, Cho, H.-S, Murakami, K.S. | | Deposit date: | 2019-07-07 | | Release date: | 2020-07-01 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.79 Å) | | Cite: | Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase.
Nat Commun, 11, 2020
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7M2U
 | | Nucleotide Excision Repair complex TFIIH Rad4-33 | | Descriptor: | CALCIUM ION, DNA repair helicase RAD25, DNA repair helicase RAD3, ... | | Authors: | van Eeuwen, T, Murakami, K. | | Deposit date: | 2021-03-17 | | Release date: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (8.2 Å) | | Cite: | Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Nat Commun, 12, 2021
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8URW
 | | Cyanobacterial RNA polymerase elongation complex with NusG and CTP | | Descriptor: | CYTIDINE-5'-TRIPHOSPHATE, DNA (40-MER), DNA-directed RNA polymerase subunit alpha, ... | | Authors: | Qayyum, M.Z, Imashimizu, M, Leanca, M, Vishwakarma, R.K, Bradley Riaz, A, Yuzenkova, Y, Murakami, K.S. | | Deposit date: | 2023-10-26 | | Release date: | 2023-12-27 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (2.79 Å) | | Cite: | Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase.
Proc.Natl.Acad.Sci.USA, 121, 2024
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8EOE
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