6A5P

RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the nucleosome transition during RNA polymerase II passage.

Kujirai, T.Ehara, H.Fujino, Y.Shirouzu, M.Sekine, S.I.Kurumizaka, H.

(2018) Science 362: 595-598

  • DOI: 10.1126/science.aau9904
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome ...

    Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.


    Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China. Electronic address: yunch@hsc.pku.edu.cn.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Electronic address: carlos.bloch@embrapa.br.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Université de Lorraine, CNRS, CRM2, Nancy, France. claude.didierjean@univ-lorraine.fr.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Université de Lorraine, INRA, IAM, Nancy, France.,Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. leslie@olemapharma.com.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia e Goiás (IFG), Luziânia, Goiás, Brazil.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Chemistry , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, Brazil.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. sfanning@uchicago.edu.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Université de Lorraine, LERMAB, Nancy, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Magnetic Resonance Center CERM , University of Florence , Via Luigi Sacconi 6 , 50019 Sesto Fiorentino, Florence , Italy.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea ygkim76@postech.ac.kr.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit
A
1743Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R4Y0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
B
1227Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4QZQ7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II third largest subunit B44, part of central core
C
304Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R7L2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B32
D
186Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R2U9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
E
214Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R3P8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
F
155Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R1V1
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit
G
171Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R9A1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
145Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R273
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit
I
115Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)Mutation(s): 0 
Gene Names: RPB9
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Go to UniProtKB:  F2QPE6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
J
72Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R009
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B12.5
K
118Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R3Z5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-alpha
L
72Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)Mutation(s): 0 
Gene Names: RPC10
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Go to UniProtKB:  F2QMI1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
a, e
139Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Histone H4
b, f
106Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
c, g
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, HIST1H2AE (H2AFM, H2AFA)
Find proteins for P04908 (Homo sapiens)
Go to Gene View: HIST1H2AB HIST1H2AE
Go to UniProtKB:  P04908
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
d, h
129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ (H2BFR)
Find proteins for P06899 (Homo sapiens)
Go to Gene View: HIST1H2BJ
Go to UniProtKB:  P06899
Entity ID: 13
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3')P11synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
DNA (198-MER)T198synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (198-MER)N198synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25116002
Japan Society for the Promotion of ScienceJapanJP15H04344
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101082
Japan Science and TechnologyJapanJPMJCR16G1
RIKEN Dynamic Structural Biology projectJapan--

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection, Database references