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- EMDB-80607: PSI with 8LHCI from Diplosphaera chodatii -

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Basic information

Entry
Database: EMDB / ID: EMD-80607
TitlePSI with 8LHCI from Diplosphaera chodatii
Map data
Sample
  • Complex: PSI with 8LHCI from Diplosphaera chodatii
Keywordsphotosystem I / LHCI / PHOTOSYNTHESIS
Biological speciesDiplosphaera chodatii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsSu XD / Wei XL / Li M
Funding support China, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesY2022038 China
Chinese Academy of SciencesYSBR-015 China
National Natural Science Foundation of China (NSFC)32171183 China
Chinese Academy of SciencesXDB37020101 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural insights into assembly and environmental adaptation of photosystem I from a lichen green alga
Authors: Su X / Shi L / Liu Z / Zhao X / Wei X / Li M
History
DepositionApr 28, 2026-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80607.png

Downloads & links

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Map

FileDownload / File: emd_80607.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 400 pix.
= 408. Å		1.02 Å/pix.
x 400 pix.
= 408. Å		1.02 Å/pix.
x 400 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.061285987 - 0.15072674
Average (Standard dev.)0.00022781025 (±0.0030430052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80607_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_80607_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 : PSI with 8LHCI from Diplosphaera chodatii

EntireName: PSI with 8LHCI from Diplosphaera chodatii
Components
  • Complex: PSI with 8LHCI from Diplosphaera chodatii

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Supramolecule #1: PSI with 8LHCI from Diplosphaera chodatii

SupramoleculeName: PSI with 8LHCI from Diplosphaera chodatii / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Diplosphaera chodatii (plant)

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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

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai Spirit / 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:

6ijo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 69264
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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