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- EMDB-35979: A tomogram of a concave region on the nucleus of a neutrophil -

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Basic information

Entry
Database: EMDB / ID: EMD-35979
TitleA tomogram of a concave region on the nucleus of a neutrophil
Map data
Sample
  • Cell: Neutrophils of mice
KeywordsLobulation / Intermediate filament / Nuclear envelope / PROTEIN FIBRIL
Biological speciesMus sp. (mice)
Methodelectron tomography / cryo EM
AuthorsLi Z / Guo Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)#31970974 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Vimentin regulates nuclear segmentation in neutrophils.
Authors: Jiaqi Liu / Zhixun Li / Meijing Li / Wenjing Du / Wolfgang Baumeister / Jing Yang / Qiang Guo /
Abstract: Granulocytes are indispensable for various immune responses. Unlike other cell types in the body, the nuclei of granulocytes, particularly neutrophils, are heavily segmented into multiple lobes. ...Granulocytes are indispensable for various immune responses. Unlike other cell types in the body, the nuclei of granulocytes, particularly neutrophils, are heavily segmented into multiple lobes. Although this distinct morphological feature has long been observed, the underlying mechanism remains incompletely characterized. In this study, we utilize cryo-electron tomography to examine the nuclei of mouse neutrophils, revealing the cytoplasmic enrichment of intermediate filaments on the concave regions of the nuclear envelope. Aided by expression profiling and immuno-electron microscopy, we then elucidate that the intermediate-filament protein vimentin is responsible for such perinuclear structures. Of importance, exogenously expressed vimentin in nonimmune cells is sufficient to form cytoplasmic filaments wrapping on the concave nuclear surface. Moreover, genetic deletion of the protein causes a significant reduction of the number of nuclear lobes in neutrophils and eosinophils, mimicking the hematological condition of the Pelger-Huët anomaly. These results have uncovered a new component establishing the nuclear segmentation of granulocytes.
History
DepositionApr 21, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35979.png

Downloads & links

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Map

FileDownload / File: emd_35979.map.gz / Format: CCP4 / Size: 749.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 19.98 Å
Density
Minimum - Maximum-16109.510000000000218 - 6622.855499999999665
Average (Standard dev.)-0.00000016776292 (±202.317350000000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960682300
Spacing682960300
CellA: 13626.359 Å / B: 19180.799 Å / C: 5994.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Neutrophils of mice

EntireName: Neutrophils of mice
Components
  • Cell: Neutrophils of mice

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Supramolecule #1: Neutrophils of mice

SupramoleculeName: Neutrophils of mice / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus sp. (mice)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.5 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.43 sec. / Average electron dose: 1.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 57

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