[English] 日本語
Yorodumi
- EMDB-55361: CryoEM structure of MraZ in complex with 4 box promoter from Myco... -

+
Open data


ID or keywords:

Loading...

-
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: Sanchez-Alba L / Varejao N / Durand A / Garcia-Pardo J / Carreras-Caballe M / Amador V / Pinyol J / Reverter D
History
DepositionOct 14, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55361.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #1

Fileemd_55361_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55361_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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)

-
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

-
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

-
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)

-
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)

-
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)

-
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)

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more