6PSQ

Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Stepwise Promoter Melting by Bacterial RNA Polymerase.

Chen, J.Chiu, C.Gopalkrishnan, S.Chen, A.Y.Olinares, P.D.B.Saecker, R.M.Winkelman, J.T.Maloney, M.F.Chait, B.T.Ross, W.Gourse, R.L.Campbell, E.A.Darst, S.A.

(2020) Mol Cell 78: 275

  • DOI: 10.1016/j.molcel.2020.02.017
  • Primary Citation of Related Structures:  
    6PSR, 6PSQ, 6PST, 6PSS, 6PSV, 6PSU, 6PSW

  • PubMed Abstract: 
  • Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure ...

    Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA. Electronic address: darst@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'A [auth J]1430Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein TraRB [auth N]72Escherichia coliMutation(s): 0 
Gene Names: traRECOK12F083
UniProt
Find proteins for P41065 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth G], D [auth H], H [auth M]329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaE [auth I]1342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (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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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDG [auth L]616Escherichia coliMutation(s): 0 
Gene Names: rpoD
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (85-MER)I [auth O]85Escherichia coli
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (85-MER)J [auth P]85Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references