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- EMDB-53132: Rubisco subtomogram average from chloroplasts of two weeks old Ph... -

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Basic information

Entry
Database: EMDB / ID: EMD-53132
TitleRubisco subtomogram average from chloroplasts of two weeks old Physcomitrium patens protonemata cells.
Map dataMap as result of PostProcessing in RELION3. The map was sharpened with a B-factor of -429 which was automatically estimated.
Sample
  • Tissue: Rubisco in chloroplasts of Physcomitrium patens protonemata.
KeywordsRubisco / Chloroplast / Physcomitrium patens / Moss / PLANT PROTEIN
Biological speciesPhyscomitrium patens (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsPoege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA ...Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / Plitzko JM / Baumeister W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)951292European Union
CitationJournal: To Be Published
Title: Making plant tissue accessible for cryo-electron tomography
Authors: Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / ...Authors: Poege M / Dickmanns M / Xu P / Li M / Schioetz OH / Kaiser COJ / Ma J / Bieber A / Capitanio C / Brenner JA / Riggi M / Miras M / Kazemein Jasemi NS / Schulze SX / Simon R / Frommer WB / Plitzko JM / Baumeister W
History
DepositionMar 13, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53132.png

Downloads & links

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Map

FileDownload / File: emd_53132.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap as result of PostProcessing in RELION3. The map was sharpened with a B-factor of -429 which was automatically estimated.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 128 pix.
= 241.92 Å		1.89 Å/pix.
x 128 pix.
= 241.92 Å		1.89 Å/pix.
x 128 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-0.75192255 - 1.4297569
Average (Standard dev.)0.009778677 (±0.11106906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 241.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53132_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the first half map as output of Refine3D in RELION3.

Fileemd_53132_half_map_1.map
AnnotationThis is the first half map as output of Refine3D in RELION3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the second half map as output of Refine3D in RELION3.

Fileemd_53132_half_map_2.map
AnnotationThis is the second half map as output of Refine3D in RELION3.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rubisco in chloroplasts of Physcomitrium patens protonemata.

EntireName: Rubisco in chloroplasts of Physcomitrium patens protonemata.
Components
  • Tissue: Rubisco in chloroplasts of Physcomitrium patens protonemata.

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Supramolecule #1: Rubisco in chloroplasts of Physcomitrium patens protonemata.

SupramoleculeName: Rubisco in chloroplasts of Physcomitrium patens protonemata.
type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Physcomitrium patens (plant) / Tissue: Protonemata

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 5.7
VitrificationCryogen name: NITROGEN
Details: Tissue was high-pressure frozen was described in the publication and the corresponding protocol..

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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) / Average electron dose: 1.7 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: 2.5 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Details: Final alignment with C4 symmetry. / Number subtomograms used: 6000
ExtractionNumber tomograms: 10 / Number images used: 55000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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