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 31CR | pdb_000031cr

Rigid body fitted Mycobacterium smegmatis RNA polymerase in complex with HelD, SigA and RbpA in State I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

HelD is a global transcription factor enhancing gene expression in rapidly growing mycobacteria.

Vankova Hausnerova, V., Kumar, D., Neva, S., Shoman, M., Schwarz, M., Modrak, M., Jirat Matejckova, J., Brazda, P., Havelkova, J., Capdevila, A.C., Sikova, M., Pospisilova, D., Halada, P., Sanderova, H., Holubova, J., Dohal, M., Prevorovsky, M., Stanek, O., Knejzlik, Z., Kouba, T., Dvorakova, V., Hnilicova, J.

(2026) Microbiol Res 315: 128759-128759

  • DOI: https://doi.org/10.1016/j.micres.2026.128759
  • Primary Citation Related Structures: 
    31CR, 31DR, 31EF

  • PubMed Abstract: 

    HelD protein, also named HelR (encoded by MSMEG_2174 in Mycobacterium smegmatis), interacts with mycobacterial RNA polymerase (RNAP) and affects rifampicin resistance in Mycobacterium abscessus. Here, we provide data on rifampicin resistance and helD presence in the genomes of other clinically relevant nontuberculous mycobacteria. We show that helD is primarily found in rapidly growing mycobacteria, such as M. smegmatis, where we detected HelD at a subset of promoters that can also associate with CarD and RbpA. Transcriptome analysis of a helD deletion strain revealed that HelD has a dual role in gene regulation: it enhances transcription during exponential growth but reduces it in stationary phase. We show that transcription downregulation in stationary phase is accompanied by decreased amounts of the transcription initiation factors RbpA and CarD. In addition, we characterized HelD-containing RNAP complexes using native cryo-EM. Based on these data, we propose that HelD acts as a general transcription factor that releases stalled RNAP complexes and dissociates RNAP from promoters. HelD demonstrates how a single protein can perform fundamentally different tasks, mediating both antibiotic resistance and efficient transcription, and thereby shaping bacterial adaptability.


  • Organizational Affiliation: 
    • Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague, Czech Republic; Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 508.96 kDa 
  • Atom Count: 29,817 
  • Modeled Residue Count: 3,831 
  • Deposited Residue Count: 4,609 
  • Unique protein chains: 7

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QSL8 
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UniProt GroupA0QSL8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore P60281 
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UniProt GroupP60281
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Reference Sequence
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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: rpoC, MSMEG_1368, MSMEI_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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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZ, MSMEG_3053, MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: sigA, MSMEG_2758
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA helicaseG [auth H]736Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_2174
EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt), 3.6.5 (UniProt)
UniProt
Find proteins for A0QUE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAH [auth J]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpA, MSMEG_3858, MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic23-05622S

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release