4XLR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.275 

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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
314Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1524Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Go to UniProtKB:  Q9EVV4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigA
F, L
347Thermus aquaticusMutation(s): 0 
Gene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Go to UniProtKB:  Q9EZJ8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
CarD-like transcriptional regulator
M, N
164Thermus thermophilus JL-18Mutation(s): 0 
Find proteins for H9ZP94 (Thermus thermophilus JL-18)
Go to UniProtKB:  H9ZP94
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (48-MER)O,R48synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
DNA (48-MER)P,S48synthetic construct
Entity ID: 9
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*GP*A)-3')Q,T4synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.275 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 289.840α = 90.00
b = 289.840β = 90.00
c = 536.340γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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