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- EMDB-51804: In situ structure of cytoplasmic microtubule of Chlamydomonas rei... -

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Basic information

Entry
Database: EMDB / ID: EMD-51804
TitleIn situ structure of cytoplasmic microtubule of Chlamydomonas reinhardtii
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
KeywordsMicrotubule / Chlamydomonas reinhardtii / in situ / CYTOSOLIC PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 4.7 Å
AuthorsChakraborty S / Obr M / Zhang X / Kelley R / Khavnekar S / Waltz F / Righetto RD / Engel B / Kotecha A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Chakraborty S / Obr M / Zhang X / Kelley R / Khavnekar S / Waltz F / Righetto RD / Engel B / Kotecha A
History
DepositionOct 11, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51804.png

Downloads & links

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Map

FileDownload / File: emd_51804.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 224 pix.
= 430.08 Å		1.92 Å/pix.
x 224 pix.
= 430.08 Å		1.92 Å/pix.
x 224 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.84
Minimum - Maximum-1.7350637 - 2.8790758
Average (Standard dev.)0.009380742 (±0.098338775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51804_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51804_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_51804_half_map_2.map
Projections & Slices
AxesZYX

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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 / Support film - Material: CARBON
VitrificationCryogen name: NITROGEN / Chamber humidity: 90 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 4.0 µm / Nominal defocus min: 1.5 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: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 14800
ExtractionNumber tomograms: 18 / Number images used: 315155 / Software - Name: STOPGAP (ver. 0.7.0) / Software - details: AMIRA template match
Final 3D classificationSoftware - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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