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- PDB-9v7u: PSI-LHCE supercomplex from Euglena gracilis. -

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Basic information

Entry
Database: PDB / ID: 9v7u
TitlePSI-LHCE supercomplex from Euglena gracilis.
Components
  • (Chloroplast light-harvesting complex I ...) x 10
  • (Chloroplast light-harvesting complex II ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 2
  • LHCE 3
  • LHCE 8
  • LHCE 9
  • Light harvesting chlorophyll a /b binding protein of PSII
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaF
KeywordsPHOTOSYNTHESIS / PSI-eLHCI / Euglena gracilis.
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex I protein / Chloroplast light-harvesting complex II protein / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center / Light harvesting chlorophyll a /b binding protein of PSII
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsBai, T.Y. / Mao, Z.Y. / Tian, L.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2026
Title: Structural basis of diadinoxanthin-Chl a/b-binding proteins in the photosystem I supercomplex of .
Authors: Tianyu Bai / Zhiyuan Mao / Dapeng Sun / Yang Tang / Ziqiu Lu / Fei Ma / Bingxin Ma / Jinghua Chen / Weiwei Wang / Yuelin Li / Shufang Liu / Yi Yang / Yumei Wang / Lirong Tian /
Abstract: is a phototrophic flagellate that has evolved through secondary endosymbiotic events and belongs to green-lineage organisms. We report a unique structure of photosystem I-light harvesting complex I ... is a phototrophic flagellate that has evolved through secondary endosymbiotic events and belongs to green-lineage organisms. We report a unique structure of photosystem I-light harvesting complex I (PSI-LHCI) supercomplex from at a 2.23-angstrom resolution by cryo-electron microscopy. The supercomplex is composed of 8 core subunits and 16 LHCIs and exhibits distinctive structural features compared to its counterparts in green algae and plants. The LHCI subunits encircle the core complex, forming a two-layered arrangement that comprises six pairs of tightly packed heterodimers. Specifically, the 16 LHCIs consist of 4 diadinoxanthin-chlorophyll (Chl) a/b-binding antennae (Lhcbm) and 12 diadinoxanthin-Chl a-binding antennae (Lhca), and they exhibit characteristic pigment compositions combining features of green- and red-lineage organisms. These findings provide a robust structural foundation for elucidating the mechanisms of light harvesting and energy transfer as well as insights into the evolutionary changes of green-lineage PSI-LHCI.
History
DepositionMay 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PsaF
J: Photosystem I reaction center subunit IX
M: Photosystem I reaction center subunit XII
a: Chloroplast light-harvesting complex I protein
b: Chloroplast light-harvesting complex I protein
c: LHCE 3
d: Light harvesting chlorophyll a /b binding protein of PSII
e: Chloroplast light-harvesting complex II protein
h: LHCE 8
i: LHCE 9
j: Chloroplast light-harvesting complex I protein
k: Chloroplast light-harvesting complex I protein
l: Chloroplast light-harvesting complex I protein
m: Chloroplast light-harvesting complex I protein
f: Chloroplast light-harvesting complex I protein, Lhca7_2
g: Chloroplast light-harvesting complex I protein
n: Chloroplast light-harvesting complex II protein
o: Chloroplast light-harvesting complex I protein
p: Chloroplast light-harvesting complex I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)842,538391
Polymers538,39324
Non-polymers304,145367
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 84073.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P19430, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82780.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P19431, photosystem I

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Protein , 8 types, 8 molecules CDEFcdhi

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8784.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P31556, photosystem I
#4: Protein PsaD


Mass: 19742.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: Protein PsaE


Mass: 6797.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#6: Protein PsaF


Mass: 17765.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein LHCE 3


Mass: 23742.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#12: Protein Light harvesting chlorophyll a /b binding protein of PSII / LHCE 4


Mass: 23581.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q39725
#14: Protein LHCE 8


Mass: 19140.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#15: Protein LHCE 9


Mass: 19198.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Photosystem I reaction center subunit ... , 2 types, 2 molecules JM

#7: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4298.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P30394
#8: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3445.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P31479

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Chloroplast light-harvesting complex I ... , 10 types, 10 molecules abjklmfgop

#9: Protein Chloroplast light-harvesting complex I protein / LHCE 1


Mass: 18071.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPE4
#10: Protein Chloroplast light-harvesting complex I protein / LHCE 2


Mass: 18403.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPE4
#16: Protein Chloroplast light-harvesting complex I protein


Mass: 20493.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD0
#17: Protein Chloroplast light-harvesting complex I protein / LHCE 11


Mass: 18959.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPC6
#18: Protein Chloroplast light-harvesting complex I protein / LHCE 12


Mass: 17778.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD7
#19: Protein Chloroplast light-harvesting complex I protein / LHCE 13


Mass: 17835.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD7
#20: Protein Chloroplast light-harvesting complex I protein, Lhca7_2 / LHCE 6


Mass: 18875.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD3
#21: Protein Chloroplast light-harvesting complex I protein / LHCE 7


Mass: 19877.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD0
#23: Protein Chloroplast light-harvesting complex I protein


Mass: 17411.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD0
#24: Protein Chloroplast light-harvesting complex I protein / LHCE 16


Mass: 15965.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPC6

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Chloroplast light-harvesting complex II ... , 2 types, 2 molecules en

#13: Protein Chloroplast light-harvesting complex II protein / LHCE 5


Mass: 21448.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPH1
#22: Protein Chloroplast light-harvesting complex II protein / LHCE 14


Mass: 19923.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPH1

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Sugars , 2 types, 4 molecules

#26: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#32: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 9 types, 363 molecules

#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 276 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#28: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2
#29: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H56
#30: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C40H54O3
#31: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#33: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H70MgN4O6

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-eLHCI / Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Source (natural)Organism: Euglena gracilis (euglena)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1crYOLOparticle selection
13Topaz3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 562173 / Symmetry type: POINT
RefinementHighest resolution: 2.63 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00458918
ELECTRON MICROSCOPYf_angle_d0.63484806
ELECTRON MICROSCOPYf_dihedral_angle_d17.1123759
ELECTRON MICROSCOPYf_chiral_restr0.0837272
ELECTRON MICROSCOPYf_plane_restr0.0058201

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