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- EMDB-19906: In situ nucleosome subtomogram average from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: EMDB / ID: EMD-19906
TitleIn situ nucleosome subtomogram average from Chlamydomonas reinhardtii
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
Keywordsnucleosome / histone / cryo-et / chlamydomonas / chromatin / tomography / dna / in situ
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 9.65 Å
AuthorsMichael AK / Righetto RD / Obr M / van der Stappen P / Lamm L / Khavnekar S / Kotecha A / Engel BD
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss State Secretariat for Education, Research and Innovation Switzerland
CitationJournal: Biorxiv / Year: 2024
Title: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Kelley R / Khavnekar S / Righetto RD / Heebner J / Obr M / Zhang X / Chakraborty S / Tagiltsev G / Michael AK / van Dorst S / Waltz F / McCafferty CL / Lamm L / Zufferey S / Van der Stappen ...Authors: Kelley R / Khavnekar S / Righetto RD / Heebner J / Obr M / Zhang X / Chakraborty S / Tagiltsev G / Michael AK / van Dorst S / Waltz F / McCafferty CL / Lamm L / Zufferey S / Van der Stappen P / van den Hoek H / Wietrzynski W / Harar P / Wan W / Briggs JA / Plitzko JM / Engel BD / Kotecha A
History
DepositionMar 21, 2024-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19906.png

Downloads & links

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Map

FileDownload / File: emd_19906.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 128 pix.
= 250.88 Å		1.96 Å/pix.
x 128 pix.
= 250.88 Å		1.96 Å/pix.
x 128 pix.
= 250.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0005
Minimum - Maximum-0.0021462664 - 0.008799426
Average (Standard dev.)0.0000011970895 (±0.00017923623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 250.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19906_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19906_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19906_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Software - details: M / Number subtomograms used: 23878
ExtractionNumber tomograms: 126 / Number images used: 223507 / Method: Template Matching
Software:
Namedetails
STOPGAP (ver. 0.7.1)
PyTom (ver. 0.5.0)pytom-match-pick (GPU)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software:
Namedetails
RELION (ver. 3.1.4)
Warp (ver. 1.0.9)M
FSC plot (resolution estimation)

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