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: https://doi.org/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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2A [auth M],
H [auth S]		136Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1B [auth Q],
C [auth V]		130Xenopus laevisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth O],
I [auth U]		103Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1G [auth R],
J [auth W]		123Xenopus laevisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1K [auth A]1,733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150
EC: 2.7.7.6
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2L [auth B]1,224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2, RPB150, RPO22, YOR151C
EC: 2.7.7.6
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3M [auth C]348Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3, YIL021W
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4N [auth D]221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4, YJL140W, J0654
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1O [auth E]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2P [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26, RPB6, YPR187W, P9677.8
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7Q [auth G]171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7, YDR404C, D9509.22
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3R [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8, YOR224C, YOR50-14
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9S [auth I]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9, YGL070C
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5T [auth J]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10, YOR210W
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11U [auth K]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11, YOL005C
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4V [auth L]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (170-MER)D [auth T]169synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (158-MER)E [auth N]160synthetic construct
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Entity ID: 19
MoleculeChains LengthOrganismImage
RNAW [auth P]10synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth C]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth B],
BA [auth C],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth L],
X [auth A],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
Z [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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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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  (Full details and data files)

  • 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