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- EMDB-8157: Electron cryotomogram of a cryosectioned budding yeast S. cerevis... -

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Basic information

Entry
Database: EMDB / ID: EMD-8157
TitleElectron cryotomogram of a cryosectioned budding yeast S. cerevisiae cell
Map dataNone
Sample
  • Cell: Saccharomyces cerevisiae cryosection
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsLu G
CitationJournal: Mol Biol Cell / Year: 2016
Title: Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo.
Authors: Chen Chen / Hong Hwa Lim / Jian Shi / Sachiko Tamura / Kazuhiro Maeshima / Uttam Surana / Lu Gan /
Abstract: Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution ...Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin-nucleosomes-are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an "open" configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.
History
DepositionApr 21, 2016-
Header (metadata) releaseSep 14, 2016-
Map releaseSep 14, 2016-
UpdateNov 16, 2016-
Current statusNov 16, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
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  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_8157.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 9.12 Å
Density
Minimum - Maximum-5209. - 3980.
Average (Standard dev.)200.080829999999992 (±165.495679999999993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-47708
Dimensions36164096250
Spacing40963616250
CellA: 37355.52 Å / B: 32977.918 Å / C: 2280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z9.129.11999944690279.12
M x/y/z40963616250
origin x/y/z0.0000.0000.000
length x/y/z37355.52032977.9182280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS0-4778
NC/NR/NS40963616250
D min/max/mean-5209.0003980.000200.081

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae cryosection

EntireName: Saccharomyces cerevisiae cryosection
Components
  • Cell: Saccharomyces cerevisiae cryosection

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Supramolecule #1: Saccharomyces cerevisiae cryosection

SupramoleculeName: Saccharomyces cerevisiae cryosection / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: US1375 / Organ: Saccharomyces cerevisiae

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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: 6.5
GridModel: Protochips CF200-Cu / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is HPF Compact 01. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION ...Details: The value given for _emd_high_pressure_freezing.instrument is HPF Compact 01. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica UC7/FC7 / Ultramicrotomy - Temperature: 123 K / Ultramicrotomy - Final thickness: 150
Fiducial markerManufacturer: Sigma / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 15.0 µm / Calibrated magnification: 15678 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 10.0 µm / Nominal magnification: 8700
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 / Number grids imaged: 1 / Number real images: 62 / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: IMOD (ver. 4.8)
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.8) / Number images used: 62

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