6R9G

Structural basis of transcription inhibition by the DNA mimic Ocr protein of bacteriophage T7


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7.

Ye, F.Kotta-Loizou, I.Jovanovic, M.Liu, X.Dryden, D.T.Buck, M.Zhang, X.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.52125
  • Primary Citation of Related Structures:  
    6R9G

  • PubMed Abstract: 

    Bacteriophage T7 infects Escherichia coli and evades the host restriction/modification system. The Ocr protein of T7 was shown to exist as a dimer mimicking DNA and to bind to host restriction enzymes, thus preventing the degradation of the viral genome by the host. Here we report that Ocr can also inhibit host transcription by directly binding to bacterial RNA polymerase (RNAP) and competing with the recruitment of RNAP by sigma factors. Using cryo electron microscopy, we determined the structures of Ocr bound to RNAP. The structures show that an Ocr dimer binds to RNAP in the cleft, where key regions of sigma bind and where DNA resides during transcription synthesis, thus providing a structural basis for the transcription inhibition. Our results reveal the versatility of Ocr in interfering with host systems and suggest possible strategies that could be exploited in adopting DNA mimicry as a basis for forming novel antibiotics.


  • Organizational Affiliation

    Section of Structural Biology, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
Entity Groups  
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UniProt GroupP0A8T7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Overcome classical restriction gp0.3F [auth G],
G [auth F]
117Escherichia phage T7Mutation(s): 0 
Gene Names: 0.3
UniProt
Find proteins for P03775 (Escherichia phage T7)
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Go to UniProtKB:  P03775
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UniProt GroupP03775
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10.1
MODEL REFINEMENTCCP4 package7

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N007816

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release