9SX6 | pdb_00009sx6

CryoEM structure of the octamer MraZ in complex with 1 box promoter from Mycoplasma genitalium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium.

Sanchez-Alba, L.Varejao, N.Durand, A.Garcia-Pardo, J.Carreras-Caballe, M.Amador, V.Pinyol, J.Reverter, D.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-68809-2
  • Primary Citation of Related Structures:  
    9QLG, 9QLR, 9R4J, 9SX6, 9SZ7

  • PubMed Abstract: 

    Cell division is a central process in all living organisms and requires the coordinated action of many proteins and regulatory elements. In most bacteria, the division and cell wall (dcw) gene cluster is regulated by the first gene of the dcw operon, mraZ, a highly conserved DNA-binding transcriptional regulator. Here we report the structural basis of MraZ transcriptional regulation by the resolution of three different cryo-EM structures of MraZ in complex with the upstream promoter region of the dcw cluster from Mycoplasma genitalium at 3.36, 3.57 and 3.87 Å resolution. The structures reveal the specific interactions between MraZ DNA-binding motif and nucleobases of the binding boxes, which induces distortion in the MraZ octamer to enable the interaction with the four repetitive binding boxes of the promoter DNA. The "cradle-like" DNA-binding motif of MraZ exposes three highly conserved basic residues, Lys13, Arg15 and Arg86, which are essential for binding to the consensus sequence of its cognate promoter. Ultimately, the mechanism behind MraZ's DNA binding and regulation of the dcw operon could be translated to other species, working as a general mechanism for the regulation of dcw gene cluster in bacteria.


  • Organizational Affiliation
    • Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular. Universitat Autònoma de, Barcelona, Bellaterra, Spain.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator MraZ160Mycoplasmoides genitaliumMutation(s): 0 
Gene Names: mraZMG221
UniProt
Find proteins for P47463 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37))
Explore P47463 
Go to UniProtKB:  P47463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47463
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)I [auth Y]29Mycoplasmoides genitalium
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (29-MER)J [auth Z]29Mycoplasmoides genitalium
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION
RECONSTRUCTIONEMReady

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2021-124602OB-I00
Instruct-ERIC Center (Strasbourg Centre)France--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references
  • Version 1.2: 2026-03-18
    Changes: Data collection, Database references