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- PDB-9uov: PSI-8 FCPI supercomplex from haptophyte Chrysotila roscoffensis -

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Entry
Database: PDB / ID: 9uov
TitlePSI-8 FCPI supercomplex from haptophyte Chrysotila roscoffensis
Components
  • (Fucoxanthin chlorophyll a/c binding protein ...) x 8
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center (psaC)
KeywordsPHOTOSYNTHESIS / photosystem I / chlorophyll / light-harvesting complex / biogenesis / assembly / LHCI / FCPI / coccolithophore / haptophyte
Function / homology
Function and homology information


Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD
Similarity search - Component
Biological speciesChrysotila roscoffensis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsLa Rocca, R. / Tsai, P.-C. / Kato, K. / Nakajima, Y. / Akita, F. / Shen, J.-R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Multiple structures of photosystem I-FCPI supercomplexes from a coccolithophore alga reveal a modular antenna organization.
Authors: Romain La Rocca / Pi-Cheng Tsai / Koji Kato / Yoshiki Nakajima / Fusamichi Akita / Jian-Ren Shen /
Abstract: Photosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. ...Photosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. Various numbers and organizations of both PSI core and LHCI subunits are observed in various organisms. A subgroup of haptophytes named coccolithophores play a major role in marine carbon cycle and CaCO production, and the light-harvesting antennas of them are named FCPs (fucoxanthin-chlorophyll a/c binding protein) because they bind chlorophyll c and fucoxanthin in addition to chlorophyll a. A structure of a large PSI-FCPI supercomplex containing 38 FCPI subunits has been reported from a coccolithophore Emiliania huxleyi recently (L. Shen et al., Science 389, eadv2132, 2025). Here we solved five cryo-electron microscopy (cryo-EM) structures of PSI-FCPI supercomplexes isolated from another coccolithophore Chrysotila roscoffensis with different detergents at resolutions ranging from 2.3 to 1.7 Å. These structures represent discrete PSI-FCPIs containing 1, 4, 6, 8 and 9 FCPI subunits, with FCPIs arranged in a modular fashion. Association of each FCPI module to the PSI core, as well as the arrangement of protein subunits and pigments, are revealed. Contributions of individual antenna modules to excitation energy transfer were calculated and compared with PSI-FCPI supercomplexes from other species of coccolithophores and haptophytes. These results pinpoint the assembly of stable PSI-FCPI supercomplexes in C. roscoffensis and provide insights into how antenna modules contribute to energy transfer in coccolithophores.
History
DepositionApr 26, 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: 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: Mask / Part number: 1 / Data content type: Mask / 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 (psaA)
B: Photosystem I P700 chlorophyll a apoprotein A2 (psaB)
C: Photosystem I iron-sulfur center (psaC)
D: Photosystem I reaction center subunit II (psaD)
E: Photosystem I reaction center subunit IV (psaE)
F: Photosystem I reaction center subunit III (psaF)
I: Photosystem I reaction center subunit VIII (psaI)
J: Photosystem I reaction center subunit IX (psaJ)
L: Photosystem I reaction center subunit XI (psaL)
M: Photosystem I reaction center subunit XII (psaM)
O: Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)
P: Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)
Q: Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)
R: Photosystem I reaction center subunit psaR
S: Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)
U: Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)
G: Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)
H: Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)
T: Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)624,920269
Polymers425,72519
Non-polymers199,194250
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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 (psaA)


Mass: 83368.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 (psaB)


Mass: 82002.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLMR

#4: Protein Photosystem I reaction center subunit II (psaD)


Mass: 15936.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#5: Protein Photosystem I reaction center subunit IV (psaE)


Mass: 7342.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#6: Protein Photosystem I reaction center subunit III (psaF)


Mass: 20163.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#7: Protein/peptide Photosystem I reaction center subunit VIII (psaI)


Mass: 3900.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#8: Protein/peptide Photosystem I reaction center subunit IX (psaJ)


Mass: 4340.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#9: Protein Photosystem I reaction center subunit XI (psaL)


Mass: 15045.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#10: Protein/peptide Photosystem I reaction center subunit XII (psaM)


Mass: 3082.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#14: Protein Photosystem I reaction center subunit psaR


Mass: 9637.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)

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Fucoxanthin chlorophyll a/c binding protein ... , 8 types, 8 molecules OPQSUGHT

#11: Protein Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)


Mass: 21458.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#12: Protein Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)


Mass: 24382.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#13: Protein Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)


Mass: 21064.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#15: Protein Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)


Mass: 22708.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#16: Protein Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)


Mass: 20547.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#17: Protein Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)


Mass: 22153.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#18: Protein Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)


Mass: 18375.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#19: Protein Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)


Mass: 21379.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)

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Protein / Sugars , 2 types, 2 molecules C

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#3: Protein Photosystem I iron-sulfur center (psaC)


Mass: 8836.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)

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Non-polymers , 12 types, 478 molecules

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


Mass: 893.489 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#21: 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
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: 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
#25: 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
#26: 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.: 30 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#28: 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.: 2 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding protein I (FCPI) supercomplex from haptophyte Chrysotila roscoffensis
Type: COMPLEX / Details: PSI-8 FCPI supercomplex. / Entity ID: #8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-(N-morpholino)ethanesulfonic acidMES1
250 mMsodium chlorideNaCl1
31 mM[6-[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-3,4,5-trihydroxyoxan-2-yl]methyl dodecanoateEDTA1
40.05 %sucrose monolaurateSML1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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 magnification: 165000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17450 / Algorithm: FOURIER SPACE / Num. of class averages: 12 / Symmetry type: POINT

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