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- EMDB-63098: The consensus map of the Lhcb8-C2S2 PSII-LHCII supercomplex from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63098
TitleThe consensus map of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Map data
Sample
  • Complex: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
KeywordsPhotosystem II / light harvesting / photoacclimation / stress-induced antennae / cryo-EM / PHOTOSYNTHESIS
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhou Q / Caferri R / Shan JY / Amelii A / Bassi R / Liu ZF
Funding supportEuropean Union, China, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
National Natural Science Foundation of China (NSFC) China
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2025
Title: A stress-induced paralog of Lhcb4 controls the photosystem II functional architecture in Arabidopsis thaliana
Authors: Caferri R / Zhou Q / Amelii A / Shan J / Liu Z / Bassi R
History
DepositionJan 11, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63098.png

Downloads & links

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Map

FileDownload / File: emd_63098.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.7045517 - 3.426418
Average (Standard dev.)0.0008552643 (±0.1217432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63098_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63098_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 : Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from ...

EntireName: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
Components
  • Complex: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana

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Supramolecule #1: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from ...

SupramoleculeName: Cryo-EM structure of the Lhcb8-C2S2 PSII-LHCII supercomplex from Arabidopsis thaliana
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7oui

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104217
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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