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- PDB-9sx6: CryoEM structure of the octamer MraZ in complex with 1 box promot... -

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Basic information

Entry
Database: PDB / ID: 9sx6
TitleCryoEM structure of the octamer MraZ in complex with 1 box promoter from Mycoplasma genitalium
Components
  • DNA (28-MER)
  • DNA (29-MER)
  • Transcriptional regulator MraZ
KeywordsDNA BINDING PROTEIN / MraZ / transcription factor
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / nucleoid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasmoides genitalium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsReverter, D. / Sanchez-Alba, L. / Durand, A.
Funding support Spain, France, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-124602OB-I00 Spain
Instruct-ERIC Center (Strasbourg Centre) France
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium.
Authors: Lucía Sánchez-Alba / Nathalia Varejão / Alexandre Durand / Javier García-Pardo / Maria Carreras-Caballé / Virginia Amador / Jaume Pinyol / David Reverter /
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 ...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.
History
DepositionOct 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 1.2Mar 18, 2026Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.2Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator MraZ
H: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ
B: Transcriptional regulator MraZ
E: Transcriptional regulator MraZ
D: Transcriptional regulator MraZ
G: Transcriptional regulator MraZ
F: Transcriptional regulator MraZ
Y: DNA (28-MER)
Z: DNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)164,76810
Polymers164,76810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transcriptional regulator MraZ


Mass: 18367.730 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides genitalium (bacteria) / Gene: mraZ, MG221 / Production host: Escherichia coli (E. coli) / References: UniProt: P47463
#2: DNA chain DNA (28-MER)


Mass: 9064.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasmoides genitalium (bacteria)
#3: DNA chain DNA (29-MER)


Mass: 8761.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasmoides genitalium (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between Octamer MraZ and 1 Box of the promoter region from Mycoplasma genitalium
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycoplasmoides genitalium (bacteria) / Strain: G37
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mMSodium chlorideNaCl1
220 mMTrisTris1
31 mMEDTAEDTA1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 44.48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9195
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9particle selection
2RELION5particle selection
3cryoSPARC4.2.1particle selection
4SerialEMimage acquisition
6CTFFINDCTF correction
11PHENIX1.21.2_5419model refinement
15RELION3D reconstruction
16EMReady3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49625 / Symmetry type: POINT
RefinementHighest resolution: 3.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410427
ELECTRON MICROSCOPYf_angle_d0.66214335
ELECTRON MICROSCOPYf_dihedral_angle_d21.5571867
ELECTRON MICROSCOPYf_chiral_restr0.0441632
ELECTRON MICROSCOPYf_plane_restr0.0041658

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