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. 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; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
Synthetic RNAM [auth R]9synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
Synthetic DNAN [auth S]45synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
Synthetic DNAO [auth U]45synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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P [auth A]
Q [auth A]
T [auth B]
U [auth C]
V [auth C]
P [auth A],
Q [auth A],
T [auth B],
U [auth C],
V [auth C],
W [auth I],
X [auth I],
Y [auth J],
Z [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
R [auth A],
S [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description