6I84

Structure of transcribing RNA polymerase II-nucleosome complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Structure of transcribing RNA polymerase II-nucleosome complex.

Farnung, L., Vos, S.M., Cramer, P.

(2018) Nat Commun 9: 5432-5432

  • DOI: 10.1038/s41467-018-07870-y
  • Primary Citation of Related Structures:  
    6I84

  • PubMed Abstract: 

    • Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged ...

    Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription.

    Organizational Affiliation: 

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077, Göttingen, Germany. Patrick.Cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2M, S136Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1Q, V130Xenopus laevisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4O, U103Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1R, W123Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150
EC: 2.7.7.6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2, RPB150, RPO22, YOR151C
EC: 2.7.7.6
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB3C348Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3, YIL021W
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Entity ID: 10
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DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4, YJL140W, J0654
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
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DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26, RPB6, YPR187W, P9677.8
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Entity ID: 13
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DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7, YDR404C, D9509.22
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Entity ID: 14
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DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8, YOR224C, YOR50-14
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Entity ID: 15
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DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9, YGL070C
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Entity ID: 16
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DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10, YOR210W
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Entity ID: 17
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DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11, YOL005C
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Entity ID: 18
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DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (170-MER)T169synthetic construct
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (158-MER)N160synthetic construct
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    • Entity ID: 19
    MoleculeChainsLengthOrganismImage
    RNAP10synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN
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    A, B, C, I, J, L
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
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    A
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.40 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    View more in-depth experimental data

    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    European Research CouncilGermanyTransregulon (693023)
    European Molecular Biology OrganizationGermanyALTF-725-2014
    German Research FoundationGermanySFB1064
    German Research FoundationGermanySFB860

    Revision History 

    • Version 1.0: 2019-01-02
      Type: Initial release
    • Version 1.1: 2019-08-21
      Changes: Data collection, Experimental preparation
    • Version 1.2: 2019-12-18
      Changes: Other