6B6H

The cryo-EM structure of a bacterial class I transcription activation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of bacterial transcription activation.

Liu, B.Hong, C.Huang, R.K.Yu, Z.Steitz, T.A.

(2017) Science 358: 947-951

  • DOI: 10.1126/science.aao1923
  • Primary Citation of Related Structures:  
    6B6H

  • PubMed Abstract: 
  • In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms ...

    In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ 70 -RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide. The structure shows how CAP wraps the upstream DNA and how the interactions recruit RNAP. Our study provides a structural basis for understanding how activators activate transcription through the class I recruitment mechanism.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coli S88Mutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
UniProt
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
UniProt
Find proteins for P0A8T8 (Escherichia coli O157:H7)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coli S88Mutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
UniProt
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF628Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-activated global transcriptional regulator CRPG, H210Escherichia coli O157:H7Mutation(s): 0 
Gene Names: crpZ4718ECs4208
UniProt
Find proteins for P0ACK0 (Escherichia coli O157:H7)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaI75Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsLengthOrganismImage
SYNTHETIC NONTEMPLATE STRAND DNA (88-MER)J [auth 1]88Escherichia coli
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Entity ID: 9
MoleculeChainsLengthOrganismImage
SYNTHETIC TEMPLATE STRAND DNA (88-MER)K [auth 2]88Escherichia coli
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  • Entity ID: 10
    MoleculeChainsLengthOrganismImage
    NASCENT RNA 3-MERL [auth 3]3Escherichia coli
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CMP (Subject of Investigation/LOI)
    Query on CMP

    Download Ideal Coordinates CCD File 
    P [auth G], Q [auth H]ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
    C10 H12 N5 O6 P
    IVOMOUWHDPKRLL-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    M [auth D], N [auth D]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    O [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM22778

    Revision History  (Full details and data files)

    • Version 1.0: 2017-11-15
      Type: Initial release
    • Version 1.1: 2017-11-29
      Changes: Database references
    • Version 1.2: 2017-12-06
      Changes: Author supporting evidence
    • Version 1.3: 2018-07-18
      Changes: Data collection
    • Version 1.4: 2020-01-01
      Changes: Author supporting evidence, Data collection