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 1.3 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: https://doi.org/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 RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2, RPB150, RPO22, YOR151C
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3, YIL021W
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4, YJL140W, J0654
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26, RPB6, YPR187W, P9677.8
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7, YDR404C, D9509.22
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8, YOR224C, YOR50-14
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Entity ID: 9
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DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9, YGL070C
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
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DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10, YOR210W
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11, YOL005C
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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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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View more in-depth experimental data
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
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description