5TJG

Thermus aquaticus delta1.1-sigmaA holoenzyme/downstream-fork promoter complex with an open clamp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RNA polymerase motions during promoter melting.

Feklistov, A.Bae, B.Hauver, J.Lass-Napiorkowska, A.Kalesse, M.Glaus, F.Altmann, K.H.Heyduk, T.Landick, R.Darst, S.A.

(2017) Science 356: 863-866

  • DOI: 10.1126/science.aam7858
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • All cellular RNA polymerases (RNAPs), from those of bacteria to those of man, possess a clamp that can open and close, and it has been assumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on the DNA temp ...

    All cellular RNA polymerases (RNAPs), from those of bacteria to those of man, possess a clamp that can open and close, and it has been assumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on the DNA template. Here, we resolve successive motions of the initiating bacterial RNAP by studying real-time signatures of fluorescent reporters placed on RNAP and DNA in the presence of ligands locking the clamp in distinct conformations. We report evidence for an unexpected and obligatory step early in the initiation involving a transient clamp closure as a prerequisite for DNA melting. We also present a 2.6-angstrom crystal structure of a late-initiation intermediate harboring a rotationally unconstrained downstream DNA duplex within the open RNAP active site cleft. Our findings explain how RNAP thermal motions control the promoter search and drive DNA melting in the absence of external energy sources.


    Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alphaA, B314Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Explore Q9KWU8 
Go to UniProtKB:  Q9KWU8
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaC1119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Explore Q9KWU7 
Go to UniProtKB:  Q9KWU7
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'D1524Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Explore Q9KWU6 
Go to UniProtKB:  Q9KWU6
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omegaE99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Explore Q9EVV4 
Go to UniProtKB:  Q9EVV4
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigAF347Thermus aquaticusMutation(s): 0 
Gene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Explore Q9EZJ8 
Go to UniProtKB:  Q9EZJ8
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*A)-3')G31Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.098α = 104.12
b = 111.423β = 99.66
c = 143.177γ = 109.43
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-04 
  • Released Date: 2017-06-21 
  • Deposition Author(s): Darst, S.A., Bae, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1 R35 GM118130

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence