6A5P

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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

    Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitA1743Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0568
EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunitG171Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0906
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H145Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0309
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and IIIJ72Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0223
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B12.5K118Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0244
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-alphaL72Komagataella phaffii GS115Mutation(s): 0 
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3a, e139Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
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PHAROS  P84243
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Histone H4b, f106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/Ec, g133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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PHAROS  P04908
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-Jd, h129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
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PHAROS  P06899
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaB1227Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0125
EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II third largest subunit B44, part of central coreC304Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0344
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B32D186Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0104
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and IIIE214Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0157
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and IIIF155Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0434
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitI115Komagataella phaffii GS115Mutation(s): 0 
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 13
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3')P11synthetic construct

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Entity ID: 14
MoleculeChainsLengthOrganism
DNA (198-MER)T198synthetic construct

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

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other