8G1S

Cryo-EM structure of 3DVA component 1 of Escherichia coli que-PEC (paused elongation complex) RNA Polymerase minus preQ1 ligand


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand.

Chauvier, A.Porta, J.C.Deb, I.Ellinger, E.Meze, K.Frank, A.T.Ohi, M.D.Walter, N.G.

(2023) Nat Struct Mol Biol 30: 902-913

  • DOI: https://doi.org/10.1038/s41594-023-01002-x
  • Primary Citation of Related Structures:  
    8F3C, 8G00, 8G1S, 8G2W, 8G4W, 8G7E, 8G8Z

  • PubMed Abstract: 

    Folding of nascent transcripts can be modulated by the RNA polymerase (RNAP) that carries out their transcription, and vice versa. A pause of RNAP during transcription of a preQ 1 riboswitch (termed que-PEC) is stabilized by a previously characterized template consensus sequence and the ligand-free conformation of the nascent RNA. Ligand binding to the riboswitch induces RNAP pause release and downstream transcription termination; however, the mechanism by which riboswitch folding modulates pausing is unclear. Here, we report single-particle cryo-electron microscopy reconstructions of que-PEC in ligand-free and ligand-bound states. In the absence of preQ 1 , the RNA transcript is in an unexpected hyper-translocated state, preventing downstream nucleotide incorporation. Strikingly, on ligand binding, the riboswitch rotates around its helical axis, expanding the surrounding RNAP exit channel and repositioning the transcript for elongation. Our study reveals the tight coupling by which nascent RNA structures and their ligands can functionally regulate the macromolecular transcription machinery.


  • Organizational Affiliation

    Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaC [auth G],
D [auth H]
235Escherichia coliMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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UniProt GroupP0A7Z4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaE [auth I]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8V2
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UniProt GroupP0A8V2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'F [auth J]1,373Escherichia coliMutation(s): 0 
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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaG [auth K]80Escherichia coliMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A800
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UniProt GroupP0A800
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (39-MER)39Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (31-MER)31Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (47-MER)H [auth R]47Bacillus subtilis
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2

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 StatesGM131922
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118524
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD020011
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD030275

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Refinement description