8F1K

SigN RNA polymerase early-melted intermediate bound to full duplex DNA fragment dhsU36 (-12T)


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

A general mechanism for transcription bubble nucleation in bacteria.

Mueller, A.U.Chen, J.Wu, M.Chiu, C.Nixon, B.T.Campbell, E.A.Darst, S.A.

(2023) Proc Natl Acad Sci U S A 120: e2220874120-e2220874120

  • DOI: https://doi.org/10.1073/pnas.2220874120
  • Primary Citation of Related Structures:  
    8F1I, 8F1J, 8F1K

  • PubMed Abstract: 

    Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ 70 , nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ 70 . By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ N -mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ N , like σ 70 , captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth G],
D [auth H]
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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UniProt GroupP0A7Z4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaE [auth I]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'F [auth J]1,430Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaG [auth K]91Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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UniProt GroupP0A800
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorH [auth M]480Escherichia coliMutation(s): 0 
Gene Names: rpoNglnFntrAb3202JW3169
UniProt
Find proteins for P24255 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (36-MER)A,
B [auth C]
36Aquifex aeolicus
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (36-MER)I [auth B],
J [auth D]
36Aquifex aeolicus
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.2.0

Structure Validation

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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: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection