4XLR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

Bae, B.Chen, J.Davis, E.Leon, K.Darst, S.A.Campbell, E.A.

(2015) Elife 4

  • DOI: 10.7554/eLife.08505
  • Primary Citation of Related Structures:  
    4XAX, 4XLR, 4XLS

  • PubMed Abstract: 
  • A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD ...

    A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.


    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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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
MoleculeChainsSequence LengthOrganismDetailsImage
CarD-like transcriptional regulatorM, N164Thermus thermophilus JL-18Mutation(s): 0 
Gene Names: TtJL18_0238
UniProt
Find proteins for H9ZP94 (Thermus thermophilus JL-18)
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UniProt GroupH9ZP94
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (48-MER)O, R 48synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (48-MER)P, S 48synthetic construct
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Entity ID: 9
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*CP*GP*A)-3')Q, T 4synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.84α = 90
b = 289.84β = 90
c = 536.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description