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- EMDB-31081: Subtomogram average of a meiotic triple helix from a pachytene S.... -

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Basic information

Entry
Database: EMDB / ID: EMD-31081
TitleSubtomogram average of a meiotic triple helix from a pachytene S. cerevisiae cell.
Map dataNKY611 meiotic triple helix
Sample
  • Complex: Subtomogram average of a triple helix from pachytene S. cerevisiae cells.
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsMa OX / Chong W / Lee JKE / Cai S / Siebert CA / Howe A / Zhang P / Shi J / Surana U / Gan L
Funding support Singapore, 3 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R-154-000-A49-114 Singapore
Ministry of Education (MoE, Singapore)R-154-000-B42-114 Singapore
Ministry of Education (MoE, Singapore)MOE2019-T2-2-045 Singapore
CitationJournal: PLoS One / Year: 2022
Title: Cryo-ET detects bundled triple helices but not ladders in meiotic budding yeast.
Authors: Olivia X Ma / Wen Guan Chong / Joy K E Lee / Shujun Cai / C Alistair Siebert / Andrew Howe / Peijun Zhang / Jian Shi / Uttam Surana / Lu Gan /
Abstract: In meiosis, cells undergo two sequential rounds of cell division, termed meiosis I and meiosis II. Textbook models of the meiosis I substage called pachytene show that nuclei have conspicuous 100-nm- ...In meiosis, cells undergo two sequential rounds of cell division, termed meiosis I and meiosis II. Textbook models of the meiosis I substage called pachytene show that nuclei have conspicuous 100-nm-wide, ladder-like synaptonemal complexes and ordered chromatin loops. It remains unknown if these cells have any other large, meiosis-related intranuclear structures. Here we present cryo-ET analysis of frozen-hydrated budding yeast cells before, during, and after pachytene. We found no cryo-ET densities that resemble dense ladder-like structures or ordered chromatin loops. Instead, we found large numbers of 12-nm-wide triple-helices that pack into ordered bundles. These structures, herein called meiotic triple helices (MTHs), are present in meiotic cells, but not in interphase cells. MTHs are enriched in the nucleus but not enriched in the cytoplasm. Bundles of MTHs form at the same timeframe as synaptonemal complexes (SCs) in wild-type cells and in mutant cells that are unable to form SCs. These results suggest that in yeast, SCs coexist with previously unreported large, ordered assemblies.
History
DepositionMar 20, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31081.png

Downloads & links

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Map

FileDownload / File: emd_31081.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNKY611 meiotic triple helix
Voxel sizeX=Y=Z: 4.61 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.1218125 - 1.3910906
Average (Standard dev.)0.018164163 (±0.29558468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 295.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_31081_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_31081_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Subtomogram average of a triple helix from pachytene S. cerevisia...

EntireName: Subtomogram average of a triple helix from pachytene S. cerevisiae cells.
Components
  • Complex: Subtomogram average of a triple helix from pachytene S. cerevisiae cells.

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Supramolecule #1: Subtomogram average of a triple helix from pachytene S. cerevisia...

SupramoleculeName: Subtomogram average of a triple helix from pachytene S. cerevisiae cells.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: NKY611 / Organelle: Nucleus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7 / Details: Sporulation medium (2% potassium acetate)
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV
Details: The Vitrobot's cup was used to condense the ethane cryogen. Crimped copper tubes containing cell paste were held ~ 3 cm above the surface of the liquid ethane, then dropped..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 18000
Specialist opticsPhase plate: VOLTA PHASE PLATE
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 13 / Number images used: 841
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Number subtomograms used: 841

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