6XLA

Cryo-EM structure of EcmrR-DNA complex in EcmrR-RPitc-3nt


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

Yang, Y.Liu, C.Zhou, W.Shi, W.Chen, M.Zhang, B.Schatz, D.G.Hu, Y.Liu, B.

(2021) Nat Commun 12: 2702-2702

  • DOI: 10.1038/s41467-021-22990-8
  • Primary Citation of Related Structures:  
    6WL5, 6XL5, 6XL6, 6XL9, 6XLA, 6XLJ, 6XLK, 6XLL, 6XLM, 6XLN

  • PubMed Abstract: 
  • Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds ...

    Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Here we report one crystal structure of a multidrug-sensing MerR family regulator EcmrR and nine cryo-electron microscopy structures that capture the EcmrR-dependent transcription process from promoter opening to initial transcription to RNA elongation. These structures reveal that EcmrR is a dual ligand-binding factor that reshapes the suboptimal 19-bp spacer DNA to enable optimal promoter recognition, sustains promoter remodeling to stabilize initial transcribing complexes, and finally dissociates from the promoter to reverse DNA remodeling and facilitate the transition to elongation. Our findings yield a comprehensive model for transcription regulation by MerR family factors and provide insights into the transition from transcription initiation to elongation.


    Organizational Affiliation

    Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA. liu00794@umn.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MerR family transcriptional regulator EcmrRA [auth G], B [auth H]268Escherichia coliMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
synthetic non-template strand DNA (54-MER)C [auth N]54Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
synthetic template strand DNA (54-MER)D [auth T]54Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
118 (Subject of Investigation/LOI)
Query on 118

Download Ideal Coordinates CCD File 
E [auth G], F [auth H]TETRAPHENYLANTIMONIUM ION
C24 H20 Sb
SZOUUWBVOLRGQM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references