6X26

Mfd-bound E.coli RNA polymerase elongation complex - L1 state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for transcription complex disruption by the Mfd translocase.

Kang, J.Y.Llewellyn, E.Chen, J.Olinares, P.D.B.Brewer, J.Chait, B.T.Campbell, E.A.Darst, S.A.

(2021) Elife 10

  • DOI: 10.7554/eLife.62117
  • Primary Citation of Related Structures:  
    6X43, 6X4W, 6X4Y, 6X2N, 6X2F, 6X26, 6X50

  • PubMed Abstract: 
  • Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC ...

    Transcription-coupled repair (TCR) is a sub-pathway of nucleotide excision repair (NER) that preferentially removes lesions from the template-strand (t-strand) that stall RNA polymerase (RNAP) elongation complexes (ECs). Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC. We used cryo-electron microscopy to visualize Mfd engaging with a stalled EC and attempting to dislodge the RNAP. We visualized seven distinct Mfd-EC complexes in both ATP and ADP-bound states. The structures explain how Mfd is remodeled from its repressed conformation, how the UvrA-interacting surface of Mfd is hidden during most of the remodeling process to prevent premature engagement with the NER pathway, how Mfd alters the RNAP conformation to facilitate disassembly, and how Mfd forms a processive translocation complex after dislodging the RNAP. Our results reveal an elaborate mechanism for how Mfd kinetically discriminates paused from stalled ECs and disassembles stalled ECs to initiate TCR.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription-repair-coupling factorA1148Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.6.4
UniProt
Find proteins for P30958 (Escherichia coli (strain K12))
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Go to UniProtKB:  P30958
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth G], C [auth H]329Escherichia coliMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth I]1342Escherichia coliMutation(s): 0 
Gene Names: rpoBAB67_4682
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth J]1407Escherichia coliMutation(s): 0 
Gene Names: rpoCBvCmsKKP036_03580
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth K]91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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  • Reference Sequence
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  • Entity ID: 6
    MoleculeChainsLengthOrganismImage
    RNA (20-MER)G [auth R]20Escherichia coli
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    Entity ID: 7
    MoleculeChainsLengthOrganismImage
    DNA (64-MER)H [auth P]64Escherichia coli
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    Entity ID: 8
    MoleculeChainsLengthOrganismImage
    DNA (64-MER)I [auth Q]64Escherichia coli
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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

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    JMAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.10 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 StatesR35 GM118130

    Revision History  (Full details and data files)

    • Version 1.0: 2021-02-03
      Type: Initial release