5FLM

Structure of transcribing mammalian RNA polymerase II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history


Literature

Structure of Transcribing Mammalian RNA Polymerase II

Bernecky, C.Herzog, F.Baumeister, W.Plitzko, J.M.Cramer, P.

(2016) Nature 529: 551

  • DOI: 10.1038/nature16482
  • Primary Citation of Related Structures:  
    5FLM

  • PubMed Abstract: 
  • RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins ...

    RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human 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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASEA1970Bos taurusMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2B1174Bos taurusMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3C275Bos taurusMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4D142Bos taurusMutation(s): 0 
Gene Names: POLR2D
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1E210Bos taurusMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 6
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2F127Bos taurusMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7G172Bos taurusMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3H150Bos taurusMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9I125Bos taurusMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5J67Bos taurusMutation(s): 0 
Gene Names: POLR2L
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11K117Bos taurusMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4L58Bos taurusMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 13
MoleculeChainsLengthOrganismImage
DNA, DNA-RNA ELONGATION SCAFFOLDM [auth N]39synthetic construct
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  • Entity ID: 14
    MoleculeChainsLengthOrganismImage
    RNA, DNA-RNA ELONGATION SCAFFOLDN [auth P]20synthetic construct
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    Entity ID: 15
    MoleculeChainsLengthOrganismImage
    DNA, DNA-RNA ELONGATION SCAFFOLDO [auth T]39synthetic construct
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    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.40 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2016-01-20
      Type: Initial release
    • Version 1.1: 2016-02-03
      Changes: Database references
    • Version 1.2: 2016-02-10
      Changes: Database references
    • Version 2.0: 2018-10-03
      Changes: Atomic model, Data collection, Derived calculations
    • Version 2.1: 2019-12-18
      Changes: Other