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- EMDB-53569: CryoEM structure of MraZ in complex with its promoter from Mycopl... -

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Basic information

Entry
Database: EMDB / ID: EMD-53569
TitleCryoEM structure of MraZ in complex with its promoter from Mycoplasma genitalium
Map dataFull map
Sample
  • Complex: Complex between four MraZ subunits and the promoter region from Mycoplasma genitalium
    • Protein or peptide: Transcriptional regulator MraZ
    • DNA: DNA (33-MER)
    • DNA: DNA (35-MER)
KeywordsMraZ / transcription factor / DNA BINDING PROTEIN
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
Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasmoides genitalium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsReverter D / Sanchez-Alba L / Durand A
Funding support Spain, France, 2 items
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
DepositionMay 7, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53569.png

Downloads & links

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Map

FileDownload / File: emd_53569.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å		0.73 Å/pix.
x 360 pix.
= 262.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000561
Minimum - Maximum-0.0074013406 - 0.010031527
Average (Standard dev.)-0.000006657068 (±0.00039225505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_53569_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53569_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between four MraZ subunits and the promoter region from M...

EntireName: Complex between four MraZ subunits and the promoter region from Mycoplasma genitalium
Components
  • Complex: Complex between four MraZ subunits and the promoter region from Mycoplasma genitalium
    • Protein or peptide: Transcriptional regulator MraZ
    • DNA: DNA (33-MER)
    • DNA: DNA (35-MER)

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Supramolecule #1: Complex between four MraZ subunits and the promoter region from M...

SupramoleculeName: Complex between four MraZ subunits and the promoter region from Mycoplasma genitalium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasmoides genitalium (bacteria) / Strain: G37

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Macromolecule #1: Transcriptional regulator MraZ

MacromoleculeName: Transcriptional regulator MraZ / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 18.49691 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MLLGTFNLTL DNKNRISLPA KLRSFFDSSI VINRGFENCL EIRKPADFES YFQTFNNFPN TQKDTRTLK RLIFANANLV ELDSANRILI PNNLISDAKL DKEIVLIGQF DHLEVWDKVQ YEQYLASSES LETVAERMKD A K

UniProtKB: Transcriptional regulator MraZ

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Macromolecule #2: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 10.29067 KDa
SequenceString:
(DT)(DT)(DT)(DA)(DA)(DA)(DA)(DG)(DT)(DG) (DT)(DC)(DG)(DC)(DA)(DA)(DA)(DG)(DT)(DG) (DT)(DG)(DA)(DC)(DA)(DA)(DA)(DG)(DT) (DG)(DG)(DA)(DA)

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Macromolecule #3: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 10.607845 KDa
SequenceString:
(DT)(DT)(DC)(DC)(DA)(DC)(DT)(DT)(DT)(DG) (DT)(DC)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DG) (DC)(DG)(DA)(DC)(DA)(DC)(DT)(DT)(DT) (DT)(DA)(DA)(DA)(DC)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
250.0 mMNaClSodium chloride
20.0 mMTrisTris
1.0 mMEDTAEDTA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9195 / Average exposure time: 3.0 sec. / Average electron dose: 44.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9qlg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, EMReady) / Number images used: 928675
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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