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- EMDB-65931: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena... -

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Basic information

Entry
Database: EMDB / ID: EMD-65931
TitleCryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
Map data
Sample
  • Complex: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
KeywordsComplex / PHOTOSYNTHESIS
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsHuang GQ / Dong SS / Sui SF / Qin XC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: The architecture and energy transfer pathways of PSI-LHCI-LHCII in the phototrophic flagellate Euglena gracilis.
Authors: Guoqiang Huang / Shishang Dong / Lin Li / Lixia Zhu / Jiayi Bai / Xing Han / Jiasheng Jiang / Jinxin Ju / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosystem I (PSI) harvests light through light-harvesting complexes (LHCs) to drive electron transfer. Euglena gracilis, a secondary endosymbiotic green alga, yet the architecture of its PSI-LHCs ...Photosystem I (PSI) harvests light through light-harvesting complexes (LHCs) to drive electron transfer. Euglena gracilis, a secondary endosymbiotic green alga, yet the architecture of its PSI-LHCs supercomplex has remained unresolved. Here, we report a 2.06 Å cryo-electron microscopy structure of the E. gracilis PSI-LHCI-LHCII supercomplex, revealing a minimal PSI core associated with ten antennas arranged in two layers on the PsaM-facing side. Each inner and outer LHC forms a face-to-face pair, while four LHCI heterodimers, stabilized by conserved Loop_23 motifs, assemble into two tetramers bridged by a central LHCI-LHCII pair. Notably, a ~ 40-residue insertion in PsaD was observed, anchoring LHC-3 and stabilizing LHC belts. Moreover, Euglena-specific chlorophylls and a distinctive arrangement of red chlorophylls establish a distinct pigment network, channeling excitation-energy into the core. These findings uncover a lineage-specific strategy for light-harvesting, highlighting how secondary plastids remodel PSI-LHCs architecture to support photosynthesis.
History
DepositionAug 21, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65931.png

Downloads & links

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Map

FileDownload / File: emd_65931.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 417.5 Å		0.84 Å/pix.
x 500 pix.
= 417.5 Å		0.84 Å/pix.
x 500 pix.
= 417.5 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.52049565 - 0.9707345
Average (Standard dev.)0.000032532702 (±0.020531753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 417.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65931_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65931_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 : Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena...

EntireName: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
Components
  • Complex: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis

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Supramolecule #1: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena...

SupramoleculeName: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Euglena gracilis (euglena)

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104987
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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