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- PDB-9uas: PSI-LHCE-LHCII from Euglena gracilis -

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Basic information

Entry
Database: PDB / ID: 9uas
TitlePSI-LHCE-LHCII from Euglena gracilis
Components
  • (Photosystem I ...) x 2
  • LhcE6
  • LhcE7
  • LhcbM2
  • LhcbM4.10
  • LhcbM4.6
  • LhcbM8
  • Lhce10
  • Lhce11
  • Lhce5
  • Lhce5.7
  • Lhce7.3
  • Lhce8
  • PsaA
  • PsaD
  • PsaE
  • PsaF
  • PsaJ
  • PsaM
KeywordsPHOTOSYNTHESIS / PSI / LHCE / 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 protein PsaC / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. ...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 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 ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NEX / 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 II protein / Photosystem I P700 chlorophyll a apoprotein A2 / 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: 2.35 Å
AuthorsFeng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: PSI-LHCE-LHCII from Euglena gracilis
Authors: Feng, Y.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBJ
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: FSC / Data content type: FSC / 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
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: PsaD
E: PsaE
F: PsaF
G: Lhce5.7
H: Lhce7.3
I: Lhce5
J: PsaJ
K: LhcE6
L: Lhce8
M: PsaM
N: Lhce5
O: LhcE7
P: Lhce5.7
Q: LhcE6
R: Lhce8
S: Lhce10
T: Lhce11
U: LhcbM4.6
V: LhcbM4.10
W: LhcbM2
X: LhcbM8
A: PsaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)936,609460
Polymers587,52224
Non-polymers349,086436
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 ... , 2 types, 2 molecules BC

#1: 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
#2: 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

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Protein , 16 types, 20 molecules DEFGPHINKQLROSTUVWXA

#3: Protein PsaD


Mass: 21417.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#4: Protein PsaE


Mass: 17581.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: Protein PsaF


Mass: 34298.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#6: Protein Lhce5.7


Mass: 19693.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPC6
#7: Protein Lhce7.3


Mass: 20127.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPC6
#8: Protein Lhce5


Mass: 19522.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPD7
#10: Protein LhcE6


Mass: 20605.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein Lhce8


Mass: 20266.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPC6
#13: Protein LhcE7


Mass: 19413.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#14: Protein Lhce10


Mass: 19491.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPE4
#15: Protein Lhce11


Mass: 18799.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPE4
#16: Protein LhcbM4.6


Mass: 22441.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPH1
#17: Protein LhcbM4.10


Mass: 21355.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#18: Protein LhcbM2


Mass: 24432.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q39725
#19: Protein LhcbM8


Mass: 23914.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#20: Protein PsaA


Mass: 84550.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Protein/peptide , 2 types, 2 molecules JM

#9: Protein/peptide PsaJ


Mass: 4512.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#12: Protein/peptide PsaM / 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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Sugars , 2 types, 39 molecules

#25: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#27: Sugar...
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 11 types, 397 molecules

#21: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 279 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#24: 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.: 42 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#30: 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 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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-LHCE-LHCI from Euglena gracilis / Type: COMPLEX / Entity ID: #1-#20 / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.20.1_4487:model refinement
13crYOLO3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51871 / Symmetry type: POINT

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