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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: Sanchez-Alba L / Varejao N / Durand A / Garcia-Pardo J / Carreras-Caballe M / Amador V / Pinyol J / Reverter D
History
DepositionMay 7, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 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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