8FVR

CryoEM structure of E.coli transcription elongation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Control of transcription elongation and DNA repair by alarmone ppGpp.

Weaver, J.W.Proshkin, S.Duan, W.Epshtein, V.Gowder, M.Bharati, B.K.Afanaseva, E.Mironov, A.Serganov, A.Nudler, E.

(2023) Nat Struct Mol Biol 30: 600-607

  • DOI: https://doi.org/10.1038/s41594-023-00948-2
  • Primary Citation of Related Structures:  
    8FVR, 8FVW

  • PubMed Abstract: 

    Second messenger (p)ppGpp (collectively guanosine tetraphosphate and guanosine pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating transcription initiation. More recently, ppGpp has been implicated in coupling transcription and DNA repair; however, the mechanism of ppGpp engagement remained elusive. Here we present structural, biochemical and genetic evidence that ppGpp controls Escherichia coli RNA polymerase (RNAP) during elongation via a specific site that is nonfunctional during initiation. Structure-guided mutagenesis renders the elongation (but not initiation) complex unresponsive to ppGpp and increases bacterial sensitivity to genotoxic agents and ultraviolet radiation. Thus, ppGpp binds RNAP at sites with distinct functions in initiation and elongation, with the latter being important for promoting DNA repair. Our data provide insights on the molecular mechanism of ppGpp-mediated adaptation during stress, and further highlight the intricate relationships between genome stability, stress responses and transcription.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA [auth D],
B [auth E]
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
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth F]1,342Escherichia 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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D [auth G]1,416Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8T7
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE [auth H]91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (53-MER)F [auth A]53Escherichia coli
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (16-MER)G [auth C]16Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (53-MER)H [auth B]53Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCootv0.8.9.2
MODEL REFINEMENTPHENIXv1.17.1
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088118-09
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM112940
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM126891
Blavatnik Family FoundationUnited States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection