5IPL

SigmaS-transcription initiation complex with 4-nt nascent RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism.

Liu, B.Zuo, Y.Steitz, T.A.

(2016) Proc Natl Acad Sci U S A 113: 4051-4056

  • DOI: 10.1073/pnas.1520555113
  • Primary Citation of Related Structures:  
    5IPM, 5IPL, 5IPN

  • PubMed Abstract: 
  • In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via ...

    In bacteria, multiple σ factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the σ factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures of E coli transcription initiation complexes (TICs) containing the stress-responsive σ(S) factor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (σ(S)-TIC) at about 3.9-Å resolution. The structures show the 3D topology of the σ(S) factor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, σ(S)-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these σ(S)-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520; Department of Chemistry, Yale University, New Haven, CT 06520 thomas.steitz@yale.edu yuhong.zuo@yale.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB242Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coliMutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE90Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoSF336Escherichia coliMutation(s): 0 
Gene Names: rpoSappRkatFnurotsXsigSb2741JW5437
Find proteins for P13445 (Escherichia coli (strain K12))
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Go to UniProtKB:  P13445
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
synthetic nontemplate strand DNA (50-MER)150synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
synthetic template strand DNA (50-MER)250synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 8
    MoleculeChainsLengthOrganismImage
    nascent RNA 4-mer34synthetic construct
    Small Molecules
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.60 Å
    • R-Value Free: 0.293 
    • R-Value Work: 0.247 
    • R-Value Observed: 0.249 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 131.71α = 90
    b = 152.671β = 90
    c = 226.698γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2016-03-30
      Type: Initial release
    • Version 1.1: 2016-04-13
      Changes: Database references
    • Version 1.2: 2016-06-22
      Changes: Database references