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- EMDB-61019: Subtomogram averaging of the C2S2M2L2-type PSII-LHCII supercomple... -

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Basic information

Entry
Database: EMDB / ID: EMD-61019
TitleSubtomogram averaging of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Map dataC2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii, 24.2 A. (contour level 1.95 for transmembrane region, 0.3 for extramembrane region)
Sample
  • Cell: Chlamydomonas reinhardtii
Keywordscomplex / PHOTOSYNTHESIS
Biological speciesChlamydomonas reihardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 24.2 Å
AuthorsLi X / Yan X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241023 and 92254306 China
Citation
Journal: Nat Commun / Year: 2025
Title: MPicker: visualizing and picking membrane proteins for cryo-electron tomography.
Authors: Xiaofeng Yan / Shudong Li / Weilin Huang / Hao Wang / Tianfang Zhao / Mingtao Huang / Niyun Zhou / Yuan Shen / Xueming Li /
Abstract: Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in ...Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins.
#1: Journal: To Be Published
Title: MPicker: Visualizing and Picking Membrane Proteins for Cryo-Electron Tomography
Authors: Li X / Yan X
History
DepositionJul 31, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61019.png

Downloads & links

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Map

FileDownload / File: emd_61019.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii, 24.2 A. (contour level 1.95 for transmembrane region, 0.3 for extramembrane region)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.63 Å/pix.
x 140 pix.
= 508.2 Å		3.63 Å/pix.
x 140 pix.
= 508.2 Å		3.63 Å/pix.
x 140 pix.
= 508.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.95
Minimum - Maximum-2.2529328 - 2.5512264
Average (Standard dev.)0.025256032 (±0.4112912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 508.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: It is hard to see the signal directly from half maps without lowpass.

Fileemd_61019_half_map_2.map
AnnotationIt is hard to see the signal directly from half maps without lowpass.
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 reihardtii (plant) / Strain: CC-1691

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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: cell suspension
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 1846
ExtractionNumber tomograms: 4 / Number images used: 1846
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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