6EE8

Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.

Boyaci, H.Chen, J.Jansen, R.Darst, S.A.Campbell, E.A.

(2019) Nature 565: 382-385

  • DOI: 10.1038/s41586-018-0840-5
  • Primary Citation of Related Structures:  
    6EDT, 6EEC, 6EE8, 6M7J

  • PubMed Abstract: 
  • A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex 1-3 . To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site ...

    A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex 1-3 . To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed 4-6 . Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA. elizabeth.campbell@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha AB347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta C1134Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoBSAMEA2682864_01701
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta' D1326Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega E110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoZERS007672_03979ERS007703_04032ERS007720_04749ERS027652_00548ERS027654_02543ERS027656_03959ERS124361_02246
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA F531Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigAmysArpoDrpoV
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpA J111Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rbpA
Find proteins for P9WHJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding transcription factor CarD M162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: carD
Find proteins for P9WJG3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (65-MER)O90Mycobacterium tuberculosis
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (60-MER)P90Mycobacterium tuberculosis
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other