3N97

RNA polymerase alpha C-terminal domain (E. coli) and sigma region 4 (T. aq. mutant) bound to (UP,-35 element) DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element.

Lara-Gonzalez, S.Dantas Machado, A.C.Rao, S.Napoli, A.A.Birktoft, J.Di Felice, R.Rohs, R.Lawson, C.L.

(2020) Biochemistry 59: 4523-4532

  • DOI: https://doi.org/10.1021/acs.biochem.0c00571
  • Primary Citation of Related Structures:  
    3N4M, 3N97

  • PubMed Abstract: 

    We demonstrate here that the α subunit C-terminal domain of Escherichia coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of αCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A 6 -tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A 6 -tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A 6 -tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second αCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either αCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving αCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factorA,
B [auth D]
72Thermus aquaticusMutation(s): 3 
Gene Names: rpoS
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus)
Explore Q9EZJ8 
Go to UniProtKB:  Q9EZJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EZJ8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth B],
D [auth C]
84Escherichia coli K-12Mutation(s): 0 
Gene Names: b3295JW3257pezphsrpoAsez
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*GP*AP*AP*AP*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*CP*AP*TP*GP*G)-3')E [auth M]22N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*AP*TP*GP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*TP*TP*CP*C)-3')F [auth N]21N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.71α = 90
b = 86.41β = 90
c = 147.11γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-11-25
    Changes: Database references, Derived calculations
  • Version 1.3: 2020-12-23
    Changes: Database references
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description