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- EMDB-19826: MucR dodecameric oligomerization domain -

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Basic information

Entry
Database: EMDB / ID: EMD-19826
TitleMucR dodecameric oligomerization domain
Map dataLocal refined map low pass filtered at 8 A resolution
Sample
  • Complex: MucR dodecamer
KeywordsH-NS / H-NS-like / nucleoid-associated protein / DNA BINDING PROTEIN
Biological speciesBrucella abortus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChaves-Sanjuan A / Del Cont-Bernard A / Bolognesi M / Nardini M
Funding support Italy, 1 items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca2022K9SJ27 Italy
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Circular oligomeric particles formed by Ros/MucR family members mediate DNA organization in α-proteobacteria.
Authors: Antonio Chaves-Sanjuan / Gianluca D'Abrosca / Veronica Russo / Bert van Erp / Alessandro Del Cont-Bernard / Riccardo Capelli / Luciano Pirone / Martina Slapakova / Domenico Sgambati / ...Authors: Antonio Chaves-Sanjuan / Gianluca D'Abrosca / Veronica Russo / Bert van Erp / Alessandro Del Cont-Bernard / Riccardo Capelli / Luciano Pirone / Martina Slapakova / Domenico Sgambati / Roberto Fattorusso / Carla Isernia / Luigi Russo / Ian S Barton / Roy Martin Roop / Emilia M Pedone / Martino Bolognesi / Remus T Dame / Paolo V Pedone / Marco Nardini / Gaetano Malgieri / Ilaria Baglivo /
Abstract: The transcriptional regulator MucR from Brucella species controls the expression of many genes, including those involved in virulence, by binding AT-rich DNA regions. MucR and its homologs belong to ...The transcriptional regulator MucR from Brucella species controls the expression of many genes, including those involved in virulence, by binding AT-rich DNA regions. MucR and its homologs belong to the Ros/MucR family, whose members occur in α-proteobacteria. MucR is a recent addition to the family of histone-like nucleoid structuring (H-NS) proteins. Indeed, despite the lack of sequence homology, MucR bears many functional similarities with H-NS and H-NS-like proteins, structuring the bacterial genome and acting as global regulators of transcription. Here we present an integrated cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance, modeling and biochemical study shedding light on the functional architecture of MucR from Brucella abortus and its homolog Ml5 from Mesorhizobium loti. We show that MucR and Ml5 fold in a circular quaternary assembly, which allows it to bridge and condense DNA by binding AT-rich sequences. Our results show that Ros/MucR family members are a novel type of H-NS-like proteins and, based on previous studies, provide a model connecting nucleoid structure and transcription regulation in α-proteobacteria.
History
DepositionMar 12, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19826.png

Downloads & links

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Map

FileDownload / File: emd_19826.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined map low pass filtered at 8 A resolution
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 260 pix.
= 231.14 Å		0.89 Å/pix.
x 260 pix.
= 231.14 Å		0.89 Å/pix.
x 260 pix.
= 231.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.51344496 - 1.3304362
Average (Standard dev.)-0.00141943 (±0.042618982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 231.14 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19826_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Local refinement output. Unsharped map

Fileemd_19826_additional_1.map
AnnotationLocal refinement output. Unsharped map
Projections & Slices
AxesZYX

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Half map: half b

Fileemd_19826_half_map_1.map
Annotationhalf b
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half a

Fileemd_19826_half_map_2.map
Annotationhalf a
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : MucR dodecamer

EntireName: MucR dodecamer
Components
  • Complex: MucR dodecamer

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Supramolecule #1: MucR dodecamer

SupramoleculeName: MucR dodecamer / type: complex / ID: 1 / Parent: 0
Details: The reconstruction comprises the oligomerization domain of 12 protomers
Source (natural)Organism: Brucella abortus (bacteria)
Molecular weightTheoretical: 82 KDa

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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

Concentration0.9 mg/mL
BufferpH: 7.4 / Details: 20mM Tris pH 7.4, 400 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4020 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2387280
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: the final map was low pass filtered to 8A resolution
Number images used: 179035
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / Details: AB INITIO JOB
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / Details: LOCAL REFINEMENT JOB
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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