6J9E

Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with NusA and the bacteriophage protein P7


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for transcription antitermination at bacterial intrinsic terminator.

You, L.Shi, J.Shen, L.Li, L.Fang, C.Yu, C.Cheng, W.Feng, Y.Zhang, Y.

(2019) Nat Commun 10: 3048-3048

  • DOI: https://doi.org/10.1038/s41467-019-10955-x
  • Primary Citation of Related Structures:  
    6J9E, 6J9F

  • PubMed Abstract: 

    Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation-in particular transcription antitermination-is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation.


  • Organizational Affiliation

    Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
346Xanthomonas oryzae pv. oryzae PXO99AMutation(s): 0 
Gene Names: rpoAPXO_04496
EC: 2.7.7.6
UniProt
Find proteins for B2SQT4 (Xanthomonas oryzae pv. oryzae (strain PXO99A))
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Go to UniProtKB:  B2SQT4
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UniProt GroupB2SQT4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,383Xanthomonas oryzae pv. oryzae PXO99AMutation(s): 0 
Gene Names: rpoBPXO_04530
EC: 2.7.7.6
UniProt
Find proteins for B2SQQ1 (Xanthomonas oryzae pv. oryzae (strain PXO99A))
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UniProt GroupB2SQQ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,405Xanthomonas oryzae pv. oryzae PXO99AMutation(s): 0 
Gene Names: rpoCPXO_04529
EC: 2.7.7.6
UniProt
Find proteins for B2SQQ2 (Xanthomonas oryzae pv. oryzae (strain PXO99A))
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UniProt GroupB2SQQ2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega99Xanthomonas oryzae pv. oryzaeMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
UniProt
Find proteins for Q5H3R9 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
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UniProt GroupQ5H3R9
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
45LI [auth J]77Xipdecavirus Xp10Mutation(s): 0 
UniProt
Find proteins for Q8LTJ5 (Xipdecavirus Xp10)
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UniProt GroupQ8LTJ5
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusAJ [auth F]507Xanthomonas oryzae pv. oryzae PXO99AMutation(s): 0 
Gene Names: nusA
UniProt
Find proteins for A0A0K0GMR0 (Xanthomonas oryzae pv. oryzae (strain PXO99A))
Explore A0A0K0GMR0 
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UniProt GroupA0A0K0GMR0
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (29-MER)F [auth G]29synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (29-MER)G [auth H]29synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')H [auth I]20synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31822001

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Refinement description