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- EMDB-55361: CryoEM structure of MraZ in complex with 4 box promoter from Myco... -

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Basic information

Entry
Database: EMDB / ID: EMD-55361
TitleCryoEM structure of MraZ in complex with 4 box promoter from Mycoplasma genitalium
Map data
Sample
  • Complex: Complex between MraZ and 4 Box of the promoter region from Mycoplasma genitalium
    • Protein or peptide: Transcriptional regulator MraZ
    • DNA: DNA (47-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • DNA: DNA (28-MER)
    • DNA: DNA (24-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: 3.87 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
DepositionOct 14, 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_55361.png

Downloads & links

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Map

FileDownload / File: emd_55361.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 512 pix.
= 461.312 Å		0.9 Å/pix.
x 512 pix.
= 461.312 Å		0.9 Å/pix.
x 512 pix.
= 461.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.901 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0343
Minimum - Maximum-0.18310162 - 0.5143426
Average (Standard dev.)-0.00011423076 (±0.012084458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 461.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55361_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55361_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between MraZ and 4 Box of the promoter region from Mycopl...

EntireName: Complex between MraZ and 4 Box of the promoter region from Mycoplasma genitalium
Components
  • Complex: Complex between MraZ and 4 Box of the promoter region from Mycoplasma genitalium
    • Protein or peptide: Transcriptional regulator MraZ
    • DNA: DNA (47-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • DNA: DNA (28-MER)
    • DNA: DNA (24-MER)

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Supramolecule #1: Complex between MraZ and 4 Box of the promoter region from Mycopl...

SupramoleculeName: Complex between MraZ and 4 Box of 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: 10 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 18.36773 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

UniProtKB: Transcriptional regulator MraZ

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Macromolecule #2: DNA (47-MER)

MacromoleculeName: DNA (47-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 14.680518 KDa
SequenceString:
(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(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)(DA)(DA)(DA)(DA)(DT)

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Macromolecule #3: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 14.550356 KDa
SequenceString:
(DA)(DT)(DT)(DT)(DT)(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) (DC)(DT)(DT)(DT)(DT)(DA)(DT)(DC)

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Macromolecule #4: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 9.02987 KDa
SequenceString:
(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT) (DT)(DT)(DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT) (DC)(DG)(DC)(DA)(DA)(DA)(DG)(DT)(DG)

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Macromolecule #5: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 8.793694 KDa
SequenceString:
(DA)(DC)(DT)(DT)(DT)(DG)(DC)(DG)(DA)(DC) (DA)(DC)(DT)(DT)(DT)(DT)(DA)(DA)(DA)(DC) (DA)(DC)(DT)(DT)(DT)(DT)(DA)(DT)(DC)

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Macromolecule #6: DNA (28-MER)

MacromoleculeName: DNA (28-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 8.744694 KDa
SequenceString:
(DG)(DT)(DC)(DG)(DC)(DA)(DA)(DA)(DG)(DT) (DG)(DT)(DG)(DA)(DC)(DA)(DA)(DA)(DG)(DT) (DG)(DG)(DA)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #7: DNA (24-MER)

MacromoleculeName: DNA (24-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycoplasmoides genitalium (bacteria)
Molecular weightTheoretical: 7.242672 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DA)(DC) (DT)(DT)(DT)(DG)(DT)(DC)(DA)(DC)(DA)(DC) (DT)(DT)(DT)(DG)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 4002 / Average exposure time: 6.0 sec. / Average electron dose: 37.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000

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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: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, EMReady) / Number images used: 46906
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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