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Entry
Database: PDB / ID: 6ly5
TitleOrganization and energy transfer in a huge diatom PSI-FCPI supercomplex
Components
  • FCPI
  • FCPI-1
  • FCPI-10
  • FCPI-11
  • FCPI-12
  • FCPI-13
  • FCPI-14
  • FCPI-16
  • FCPI-17
  • FCPI-19
  • FCPI-2
  • FCPI-21
  • FCPI-23
  • FCPI-24
  • FCPI-3
  • FCPI-4
  • FCPI-5
  • FCPI-6
  • FCPI-7
  • FCPI-8
  • FCPI-9
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaI
  • PsaJ
  • PsaL
  • PsaM
  • PsaR
  • PsaS
KeywordsPHOTOSYNTHESIS / diatom / PSI-FCPI / photosysyem
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid ...light-harvesting complex / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / plastid / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
4Fe-4S dicluster domain / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII ...4Fe-4S dicluster domain / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / 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 / Electron transport accessory-like domain superfamily / 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
Chem-A86 / BETA-CAROTENE / 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-A86 / BETA-CAROTENE / 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 / Not-an-Elip / Fucoxanthin chlorophyll a/c protein 1 / Fucoxanthin chlorophyll a/c protein 11 / Fucoxanthin chlorophyll a/c protein 8 / photosystem I / PSI subunit V / Fucoxanthin chlorophyll a/c protein 10 / Photosystem I P700 chlorophyll a apoprotein A1 / Fucoxanthin chlorophyll a/c protein 6 / Photosystem I reaction center protein 28 / Fucoxanthin chlorophyll a/c protein 16 / Fucoxanthin chlorophyll a/c protein 9 / Fucoxanthin chlorophyll a/c protein 3 / Fucoxanthin chlorophyll a/c protein 13 / Fucoxanthin chlorophyll a/c protein 7 / Fucoxanthin chlorophyll a/c protein 4 / Fucoxanthin chlorophyll a/c protein 14 / Fucoxanthin chlorophyll a/c protein 5 / Fucoxanthin chlorophyll a/c protein 15 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II, chloroplastic / Protein fucoxanthin chlorophyl a/c protein / Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr type / Photosystem I reaction center subunit IV / Photosystem I iron-sulfur center / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsXiong, P. / Caizhe, X.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex.
Authors: Caizhe Xu / Xiong Pi / Yawen Huang / Guangye Han / Xiaobo Chen / Xiaochun Qin / Guoqiang Huang / Songhao Zhao / Yanyan Yang / Tingyun Kuang / Wenda Wang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of ...Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 Å resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 β-carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI.
History
DepositionFeb 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 2.1Sep 17, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_modification_feature ...em_admin / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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Revision 1.2Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: FCPI-7
B: FCPI-1
C: FCPI-11
D: FCPI-6
E: FCPI-5
F: FCPI-8
G: FCPI-4
H: FCPI-10
I: FCPI-3
J: FCPI-9
K: FCPI-13
L: FCPI-14
M: FCPI-16
N: FCPI-21
O: FCPI
P: FCPI
Q: FCPI
R: FCPI-24
S: FCPI-23
T: FCPI-12
W: FCPI-17
X: FCPI-17
a: PsaA
b: PsaB
c: PsaC
d: PsaD
e: PsaE
f: PsaF
i: PsaI
j: PsaJ
l: PsaL
m: PsaM
g: PsaS
h: PsaR
U: FCPI-2
V: FCPI-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,277,923625
Polymers820,43136
Non-polymers457,492589
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 30 types, 33 molecules ABCDEFGHIJKLMNOPQRSTWXabcdeflg...

#1: Protein FCPI-7


Mass: 18387.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B7P2*PLUS
#2: Protein FCPI-1


Mass: 24549.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A1E7F4Y9*PLUS
#3: Protein FCPI-11


Mass: 21114.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B024*PLUS
#4: Protein FCPI-6


Mass: 22319.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B112*PLUS
#5: Protein FCPI-5


Mass: 23502.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B3M5*PLUS
#6: Protein FCPI-8


Mass: 23085.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B492*PLUS
#7: Protein FCPI-4


Mass: 26609.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B0A4*PLUS
#8: Protein FCPI-10


Mass: 21690.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B8C0K4*PLUS
#9: Protein FCPI-3


Mass: 21176.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B150*PLUS
#10: Protein FCPI-9


Mass: 21560.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B2D5*PLUS
#11: Protein FCPI-13


Mass: 22197.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B0S3*PLUS
#12: Protein FCPI-14


Mass: 24846.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B037*PLUS
#13: Protein FCPI-16


Mass: 32645.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B2D8*PLUS
#14: Protein FCPI-21


Mass: 24252.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B7P8*PLUS
#15: Protein FCPI


Mass: 21821.184 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B125*PLUS
#16: Protein FCPI-24


Mass: 26549.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B499*PLUS
#17: Protein FCPI-23


Mass: 27555.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B7P8*PLUS
#18: Protein FCPI-12


Mass: 22340.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#19: Protein FCPI-17


Mass: 21347.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: B7FRW2*PLUS
#20: Protein PsaA


Mass: 82853.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B109*PLUS
#21: Protein PsaB


Mass: 82027.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B0E7*PLUS
#22: Protein PsaC


Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: P10793*PLUS
#23: Protein PsaD


Mass: 14943.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A5Z2K3*PLUS
#24: Protein PsaE


Mass: 7186.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: E1C9K6*PLUS
#25: Protein PsaF


Mass: 17791.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: P12355*PLUS
#28: Protein PsaL


Mass: 19030.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B0N3*PLUS
#30: Protein PsaS


Mass: 11422.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#31: Protein PsaR


Mass: 14766.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A6J4B118*PLUS
#32: Protein FCPI-2


Mass: 17351.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#33: Protein FCPI-19


Mass: 19307.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

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Protein/peptide , 3 types, 3 molecules ijm

#26: Protein/peptide PsaI


Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: P17227*PLUS
#27: Protein/peptide PsaJ


Mass: 4733.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A4GGC6*PLUS
#29: Protein/peptide PsaM


Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: Q85G73*PLUS

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Sugars , 2 types, 29 molecules

#39: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#40: 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 , 11 types, 713 molecules

#34: 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.: 35 / Source method: obtained synthetically / Formula: C40H54O3
#35: 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.: 102 / Source method: obtained synthetically / Formula: C42H58O6
#36: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 326 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#37: Chemical...
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#38: 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
#41: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#42: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C45H86O10
#43: 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
#44: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56
#45: 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
#46: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: a huge diatom PSI-FCPI supercomplex / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Buffer solutionpH: 6
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 891804
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164480 / Symmetry type: POINT

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