5NSR

Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

Glyde, R.Ye, F.Darbari, V.C.Zhang, N.Buck, M.Zhang, X.

(2017) Mol. Cell 67: 106-116.e4

  • DOI: 10.1016/j.molcel.2017.05.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcri ...

    Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.


    Organizational Affiliation

    Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK. Electronic address: xiaodong.zhang@imperial.ac.uk.,Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1342Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1407Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor
M
573Klebsiella oxytocaMutation(s): 0 
Gene Names: rpoN (ntrA)
Find proteins for P06223 (Klebsiella oxytoca)
Go to UniProtKB:  P06223
Entity ID: 6
MoleculeChainsLengthOrganism
Non-Template promoter DNAF63Klebsiella pneumoniae
Entity ID: 7
MoleculeChainsLengthOrganism
Template DNA promoterG63Klebsiella pneumoniae
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
M
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N007816
Wellcome TrustUnited KingdomWT/098412

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Data collection