6YXU

Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State I, primary channel engaged


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


Literature

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.

Kouba, T.Koval', T.Sudzinova, P.Pospisil, J.Brezovska, B.Hnilicova, J.Sanderova, H.Janouskova, M.Sikova, M.Halada, P.Sykora, M.Barvik, I.Novacek, J.Trundova, M.Duskova, J.Skalova, T.Chon, U.Murakami, K.S.Dohnalek, J.Krasny, L.

(2020) Nat Commun 11: 6419-6419

  • DOI: https://doi.org/10.1038/s41467-020-20158-4
  • Primary Citation of Related Structures:  
    6VSX, 6YXU, 6YYS

  • PubMed Abstract: 

    RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids.


  • Organizational Affiliation

    EMBL Grenoble, 71 Avenue des Martyrs, Grenoble, France. tkouba@embl.fr.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoAMSMEG_1524MSMEI_1488
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QSL8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoBMSMEG_1367MSMEI_1328
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupP60281
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoCMSMEG_1368MSMEI_1329
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QS66
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZMSMEG_3053MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated transcription factor HelDF [auth H]736Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_2174
EC: 3.6.4.12
UniProt
Find proteins for A0QUE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Refinement description