6KJ6

cryo-EM structure of Escherichia coli Crl transcription activation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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Literature

Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor.

Xu, J.Cui, K.Shen, L.Shi, J.Li, L.You, L.Fang, C.Zhao, G.Feng, Y.Yang, B.Zhang, Y.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.50928
  • Primary Citation of Related Structures:  
    6KJ6

  • PubMed Abstract: 

    σ S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σ S -mediated transcription requires a σ S -specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an Escherichia coli transcription activation complex ( E. coli Crl-TAC) comprising E. coli σ S -RNA polymerase (σ S -RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σ S S 2 ) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σ S 2 to promote the assembly of the σ S -RNAP holoenzyme and also to facilitate formation of an RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.


  • 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, Shanghai, China.


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: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB
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'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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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ
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
RNA polymerase sigma factor RpoS334Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoSappRkatFnurotsXsigSb2741JW5437
UniProt
Find proteins for P13445 (Escherichia coli (strain K12))
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UniProt GroupP13445
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Sigma factor-binding protein Crl137Escherichia coli ATCC 8739Mutation(s): 0 
Gene Names: crlEcolC_3341
UniProt
Find proteins for P24251 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (51-MER)51synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (51-MER)51synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*UP*CP*GP*A)-3')5synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31822001
Chinese Academy of SciencesChinaXDB29020000

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Refinement description