5C3E

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.

Barnes, C.O.Calero, M.Malik, I.Graham, B.W.Spahr, H.Lin, G.Cohen, A.E.Brown, I.S.Zhang, Q.Pullara, F.Trakselis, M.A.Kaplan, C.D.Calero, G.

(2015) Mol Cell 59: 258-269

  • DOI: 10.1016/j.molcel.2015.06.034
  • Primary Citation of Related Structures:  
    5C3E, 5C44, 5C4A, 5C4J, 5C4X

  • PubMed Abstract: 
  • Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble ...

    Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that "open/closed" conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation.


    Organizational Affiliation

    Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. Electronic address: guc9@pitt.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3YIL021W
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9YGL070C
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11YOL005C
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
UniProt
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    Synthetic RNAM [auth R]9synthetic construct
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    Entity ID: 14
    MoleculeChainsLengthOrganismImage
    Synthetic DNAN [auth S]45synthetic construct
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    Entity ID: 15
    MoleculeChainsLengthOrganismImage
    Synthetic DNAO [auth U]45synthetic construct
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    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.70 Å
    • R-Value Free: 0.220 
    • R-Value Work: 0.201 
    • R-Value Observed: 0.201 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 219.05α = 90
    b = 390.94β = 90
    c = 278.08γ = 90
    Software Package:
    Software NamePurpose
    BUSTER-TNTrefinement
    SCALAdata scaling
    PDB_EXTRACTdata extraction
    MOLREPphasing

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM112686
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM097260
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008424

    Revision History  (Full details and data files)

    • Version 1.0: 2015-08-26
      Type: Initial release
    • Version 1.1: 2017-09-27
      Changes: Author supporting evidence, Database references, Derived calculations
    • Version 1.2: 2019-12-25
      Changes: Author supporting evidence