4XLN

Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a bacterial RNA polymerase holoenzyme open promoter complex.

Bae, B.Feklistov, A.Lass-Napiorkowska, A.Landick, R.Darst, S.A.

(2015) Elife 4

  • DOI: 10.7554/eLife.08504
  • Primary Citation of Related Structures:  
    4XLN, 4XLP, 4XLQ

  • PubMed Abstract: 
  • Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4 ...

    Initiation of transcription is a primary means for controlling gene expression. In bacteria, the RNA polymerase (RNAP) holoenzyme binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo). We have determined crystal structures, refined to 4.14 Å-resolution, of RPo containing Thermus aquaticus RNAP holoenzyme and promoter DNA that includes the full transcription bubble. The structures, combined with biochemical analyses, reveal key features supporting the formation and maintenance of the double-strand/single-strand DNA junction at the upstream edge of the -10 element where bubble formation initiates. The results also reveal RNAP interactions with duplex DNA just upstream of the -10 element and potential protein/DNA interactions that direct the DNA template strand into the RNAP active site. Addition of an RNA primer to yield a 4 base-pair post-translocated RNA:DNA hybrid mimics an initially transcribing complex at the point where steric clash initiates abortive initiation and σ(A) dissociation.


    Organizational Affiliation

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B, G, H314Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus)
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UniProt GroupQ9KWU8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC, I1119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus)
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UniProt GroupQ9KWU7
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D, J1524Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus)
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UniProt GroupQ9KWU6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE, K99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus)
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UniProt GroupQ9EVV4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF, L347Thermus aquaticusMutation(s): 0 
Gene Names: sigA
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus)
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UniProt GroupQ9EZJ8
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (48-MER)M [auth O],
P [auth R]
48synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (48-MER)N [auth P],
Q [auth S]
48synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
RNA (5'-D(P*UP*CP*GP*A)-3')O [auth Q],
R [auth T]
4synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.282 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.259α = 90
b = 289.259β = 90
c = 536.601γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-01-13 
  • Released Date: 2015-09-23 
  • Deposition Author(s): Bae, B., Darst, S.A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM053759

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence