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- PDB-9r4j: CryoEM structure of MraZ in complex with its promoter from Mycopl... -

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Basic information

Entry
Database: PDB / ID: 9r4j
TitleCryoEM structure of MraZ in complex with its promoter from Mycoplasma genitalium
Components
  • DNA (33-MER)
  • DNA (35-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: 3.36 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: Sanchez-Alba, L. / Varejao, N. / Durand, A. / Garcia-Pardo, J. / Carreras-Caballe, M. / Amador, V. / Pinyol, J. / Reverter, D.
History
DepositionMay 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Transcriptional regulator MraZ
B: Transcriptional regulator MraZ
C: Transcriptional regulator MraZ
A: Transcriptional regulator MraZ
Y: DNA (33-MER)
Z: DNA (35-MER)


Theoretical massNumber of molelcules
Total (without water)94,8866
Polymers94,8866
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: 18496.910 Da / Num. of mol.: 4
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 (33-MER)


Mass: 10290.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasmoides genitalium (bacteria)
#3: DNA chain DNA (35-MER)


Mass: 10607.845 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 four MraZ subunits and 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
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
14RELION3D reconstruction
15EMReady3D reconstruction
16PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 928675 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076028
ELECTRON MICROSCOPYf_angle_d0.8748431
ELECTRON MICROSCOPYf_dihedral_angle_d27.2131367
ELECTRON MICROSCOPYf_chiral_restr0.053960
ELECTRON MICROSCOPYf_plane_restr0.006848

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