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- EMDB-63818: Focused refinement map of light harvesting complexes XLH2/3/4/5/6... -

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Entry
Database: EMDB / ID: EMD-63818
TitleFocused refinement map of light harvesting complexes XLH2/3/4/5/6/7/12/13 in the PSI of Tribonema minus
Map dataFocused refinement map of light harvesting complexes XLH2/3/4/5/6/7/12/13 in the PSI of Tribonema minus
Sample
  • Complex: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
KeywordsPhotosystem I / Xanthophyceae / Tribonema minus / PHOTOSYNTHESIS / MEMBRANE PROTEIN
Biological speciesTribonema minus (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsShao RQ / Pan XW
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2804400 China
National Natural Science Foundation of China (NSFC)32371269 China
National Natural Science Foundation of China (NSFC)32470247 China
Chinese Academy of Sciences2024kf05 China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Architecture of photosystem I-light-harvesting complex from the eukaryotic filamentous yellow-green alga Tribonema minus.
Authors: Ruiqi Shao / Yuqi Zou / Hui Shang / Yue Qiu / Zuxing Liang / Xiaodong Su / Shumeng Zhang / Mei Li / Xiaowei Pan /
Abstract: Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light ...Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light absorption capacity of the core complex. Throughout the evolution of oxygenic photoautotrophs, the core subunits of PSI have remained highly conserved, while LHCIs exhibit significant variability, presumably to adapt to diverse environments. This study presents a 2.82 Å resolution structure of PSI from the filamentous yellow-green alga Tribonema minus (Tm), a member of the class Xanthophyceae that evolved from red algae through endosymbiosis and is considered a promising candidate for biofuel production due to its high biomass and lipid content. Our structure reveals a supramolecular organization consisting of 12 core subunits and 13 LHCIs, here referred to as Xanthophyceae light-harvesting complexes (XLHs), along with the arrangement of pigments within the TmPSI-XLH supercomplex. A structural comparison between TmPSI-XLH and PSI-LHCI from various red lineages highlights distinctive features of TmPSI-XLH, suggesting that it represents a unique intermediate state in the PSI assembly process during the evolutionary transition from red algae to diatoms. Our findings advance the understanding of the molecular mechanisms responsible for energy transfer in Xanthophyceae PSI-XLH and the evolutionary adaptation of red lineages.
History
DepositionMar 18, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_63818.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement map of light harvesting complexes XLH2/3/4/5/6/7/12/13 in the PSI of Tribonema minus
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.42375556 - 0.7108616
Average (Standard dev.)0.00028141154 (±0.015581038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 457.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Photosystem I-Light-Harvesting Complexes from the Eukaryotic Fila...

EntireName: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
Components
  • Complex: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus

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Supramolecule #1: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Fila...

SupramoleculeName: Photosystem I-Light-Harvesting Complexes from the Eukaryotic Filamentous Yellow-Green Algae Tribonema minus
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tribonema minus (eukaryote)

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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