4YLO

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.

Zuo, Y.Steitz, T.A.

(2015) Mol Cell 58: 534-540

  • DOI: 10.1016/j.molcel.2015.03.010
  • Primary Citation of Related Structures:  
    4YLO, 4YLP, 4YLN

  • PubMed Abstract: 
  • During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for process ...

    During transcription initiation, RNA polymerase binds to promoter DNA to form an initiation complex containing a DNA bubble and enters into abortive cycles of RNA synthesis before escaping the promoter to transit into the elongation phase for processive RNA synthesis. Here we present the crystal structures of E. coli transcription initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonucleotides at about 6-Å resolution. The structures show how RNA polymerase recognizes DNA promoters that contain spacers of different lengths and reveal a bridging interaction between the 5'-triphosphate of the nascent RNA and the σ factor that may function to stabilize the short RNA-DNA hybrids during the early stage of transcription initiation. The conformation of the RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide insights into the mechanism that controls both the abortive and productive RNA synthesis.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA. Electronic address: thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABGHMN242Escherichia coliMutation(s): 0 
Gene Names: rpoAEcE24377A_3778
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Go to UniProtKB:  A7ZSI4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCIO1342Escherichia coliMutation(s): 0 
Gene Names: rpoBEcE24377A_4528
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Go to UniProtKB:  A7ZUK1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'DJP1407Escherichia coliMutation(s): 0 
Gene Names: rpoCEcE24377A_4529
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8T7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaEKQ90Escherichia coliMutation(s): 0 
Gene Names: rpoZEcE24377A_4152
EC: 2.7.7.6
Find proteins for A7ZTK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDFLR628Escherichia coliMutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NT strand DNA (49-MER)1, 4, 749synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
T strand DNA (49-MER)2, 5, 849synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')3, 6, 94synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 6.00 Å
    • R-Value Free: 0.314 
    • R-Value Work: 0.227 
    • R-Value Observed: 0.232 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 240.888α = 90
    b = 208.174β = 119.31
    c = 256.323γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2015-03-05 
    • Released Date: 2015-04-22 
    • Deposition Author(s): Zuo, Y., Steitz, T.A.

    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM057510

    Revision History 

    • Version 1.0: 2015-04-22
      Type: Initial release
    • Version 1.1: 2015-04-29
      Changes: Database references
    • Version 1.2: 2015-05-20
      Changes: Database references
    • Version 1.3: 2017-09-06
      Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
    • Version 1.4: 2019-12-25
      Changes: Author supporting evidence