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- PDB-9ygv: Photosystem I FCP Supercomplex from Macrocystis pyrifera -

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Entry
Database: PDB / ID: 9ygv
TitlePhotosystem I FCP Supercomplex from Macrocystis pyrifera
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 7
  • FCP1
  • FCP11
  • FCP15
  • FCP16
  • FCP17
  • FCP19
  • FCP2
  • FCP3
  • FCP4
  • FCP5
  • FCP6 and FCP10
  • FCP7
  • FCP8
  • FCP9 and FCP13
  • FCPA
  • FCPB
  • Photosystem I iron-sulfur center
  • PsaR
KeywordsPHOTOSYNTHESIS / Photosystem I / Brown algae / Macrocystis pyrifera
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
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 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 reaction centre subunit IV / PsaE / 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 / Electron transport accessory-like domain superfamily / 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
Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...Chem-A86 / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesMacrocystis pyrifera (giant kelp)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsMaturana, P. / Maldonado, M.
Funding support United States, 2items
OrganizationGrant numberCountry
Other privateUCD Hellman Foundation United States
Other privateC-S2C-ST-CA237 United States
CitationJournal: To Be Published
Title: Structure of a Photosystem-I-FCP supercomplex from brown alga Macrocystis pyrifera (giant kelp)
Authors: Weissman, J.D. / Maturana, P. / Riddle, R. / Wyatt, G. / Dubinin, V.G.T. / Zerbe, P. / Maldonado, M.
History
DepositionSep 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: FCP1
3: FCP3
5: FCP5
7: FCP7
8: FCP8
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
M: Photosystem I reaction center subunit XII
R: PsaR
b: FCPB
6: FCP6 and FCP10
10: FCP6 and FCP10
11: FCP11
13: FCP9 and FCP13
15: FCP15
16: FCP16
17: FCP17
19: FCP19
2: FCP2
4: FCP4
9: FCP9 and FCP13
L: Photosystem I reaction center subunit XI
a: FCPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)855,587347
Polymers604,41929
Non-polymers251,168318
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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Protein , 18 types, 20 molecules 13578CRb610111391516171924a

#1: Protein FCP1


Mass: 24077.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 1 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#2: Protein FCP3


Mass: 20481.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 3 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#3: Protein FCP5


Mass: 23108.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 5 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#4: Protein FCP7


Mass: 18366.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 7 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#5: Protein FCP8


Mass: 22788.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 8 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#8: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8780.103 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I iron-sulfur center subunit VII / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8D0, photosystem I
#15: Protein PsaR


Mass: 13673.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Macrocystis pyrifera (giant kelp)
#16: Protein FCPB


Mass: 12017.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position B in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#17: Protein FCP6 and FCP10


Mass: 22069.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 6 and 10 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#18: Protein FCP11


Mass: 22865.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 11 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#19: Protein FCP9 and FCP13


Mass: 23239.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 9 and 13 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#20: Protein FCP15


Mass: 13209.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 15 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp) / References: photosystem I
#21: Protein FCP16


Mass: 13890.110 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 16 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp) / References: photosystem I
#22: Protein FCP17


Mass: 22960.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 17 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#23: Protein FCP19


Mass: 12783.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 19 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp) / References: photosystem I
#24: Protein FCP2


Mass: 8868.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 2 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#25: Protein FCP4


Mass: 24775.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position 4 in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)
#27: Protein FCPA


Mass: 12868.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Fucoxanthin-chlorophyll a-c binding protein for position A in PSI-FCP supercomplex from Macrocystis pyrifera
Source: (natural) Macrocystis pyrifera (giant kelp)

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

#6: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83161.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I P700 chlorophyll a apoprotein A1 / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0JYL2, photosystem I
#7: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82548.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I P700 chlorophyll a apoprotein A2 / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8K8, photosystem I

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Photosystem I reaction center subunit ... , 7 types, 7 molecules DEFIJML

#9: Protein Photosystem I reaction center subunit II


Mass: 15029.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit II / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8I9
#10: Protein Photosystem I reaction center subunit IV


Mass: 6962.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit IV / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8D1
#11: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 22774.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit III / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0JY91
#12: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4007.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit VIII / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8C2
#13: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4854.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit IX / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8B4
#14: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3247.974 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit XII / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0JYJ8
#26: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 15699.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Photosystem I reaction center subunit XI / Source: (natural) Macrocystis pyrifera (giant kelp) / References: UniProt: A0A8F0F8N6

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Sugars , 1 types, 3 molecules

#34: 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, 315 molecules

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


Mass: 893.489 Da / Num. of mol.: 199 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#29: 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.: 18 / Source method: obtained synthetically / Formula: C42H58O6
#30: Chemical...
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#31: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#32: Chemical...
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56O4
#33: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C40H56
#35: 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
#36: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#37: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10

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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: Supercomplex of Macrocystis pyrifera photosystem I and FCP antenna
Type: COMPLEX
Entity ID: #1, #17-#24, #2, #25, #3-#13, #26, #14-#15, #27, #16
Source: NATURAL
Source (natural)Organism: Macrocystis pyrifera (giant kelp)
Buffer solutionpH: 7.5
Details: 15 mM HEPES, 20 mM KCl, and 5 mM NaCl, 0.01 % GDN, 0.1% Digitonin, pH 7.5.
Buffer component
IDConc.NameFormulaBuffer-ID
115 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid1
220 mMPotassium ChlorideKCl1
35 mMSodium chlorideNaCl1
40.01 % w:vglyco-diosgenin1
50.1 % w:vDigitonin1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 291.15 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 defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 4.95 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15690

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133000 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 2.47 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00755606
ELECTRON MICROSCOPYf_angle_d1.55479533
ELECTRON MICROSCOPYf_dihedral_angle_d17.37726684
ELECTRON MICROSCOPYf_chiral_restr0.0486991
ELECTRON MICROSCOPYf_plane_restr0.01212690

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