6XLN

Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent transcription


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator

Yang, Y.Liu, C.Zhou, W.Shi, W.Chen, M.Zhang, B.Schatz, D.G.Hu, Y.Liu, B.

(2021) Nat Commun 


Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha AB329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0A7Z6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta C1342Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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  • Reference Sequence
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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
Find proteins for P0A8T8 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0A8T8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega E91Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Go to UniProtKB:  B7MFL0
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
synthetic non-template strand DNA (54-MER)N54Escherichia coli O157:H7
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Entity ID: 6
MoleculeChainsLengthOrganismImage
synthetic template strand DNA (54-MER)T54Escherichia coli O157:H7
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 7
    MoleculeChainsLengthOrganismImage
    9-nt RNA transcriptR9Escherichia coli O157:H7
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    1N7
    Query on 1N7

    Download Ideal Coordinates CCD File 
    A, C
    CHAPSO
    C32 H59 N2 O8 S
    GUQQBLRVXOUDTN-XOHPMCGNSA-O
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    D
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2021-04-07
      Type: Initial release
    • Version 1.1: 2021-04-21
      Changes: Database references