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- PDB-7dr2: Structure of GraFix PSI tetramer from Cyanophora paradoxa -

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Basic information

Entry
Database: PDB / ID: 7dr2
TitleStructure of GraFix PSI tetramer from Cyanophora paradoxa
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


cyanelle 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 / oxidoreductase activity ...cyanelle 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 / oxidoreductase activity / electron transfer 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 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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / 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 / 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 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 A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit II, cyanelle
Similarity search - Component
Biological speciesCyanophora paradoxa (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKato, K. / Nagao, R. / Akita, F. / Miyazaki, N. / Shen, J.R.
Citation
Journal: Nat Commun / Year: 2022
Title: Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa.
Authors: Koji Kato / Ryo Nagao / Yoshifumi Ueno / Makio Yokono / Takehiro Suzuki / Tian-Yi Jiang / Naoshi Dohmae / Fusamichi Akita / Seiji Akimoto / Naoyuki Miyazaki / Jian-Ren Shen /
Abstract: Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable ...Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-Å resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90°, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.
#1: Journal: Biorxiv / Year: 2022
Title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Authors: Kato, K. / Nagao, R. / Ueno, Y. / Yokono, M. / Suzuki, T. / Jiang, T.Y. / Dohmae, N. / Akita, F. / Akimoto, S. / Miyazaki, N. / Shen, J.R.
History
DepositionDec 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.0Feb 16, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 16, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 16, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 16, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.journal_id_ISSN / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Sep 17, 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: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_id_ISSN / _em_admin.last_update
Revision 1.2Nov 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
aA: Photosystem I P700 chlorophyll a apoprotein A1
aB: Photosystem I P700 chlorophyll a apoprotein A2
aC: Photosystem I iron-sulfur center
aD: Photosystem I reaction center subunit II, cyanelle
aE: Photosystem I reaction center subunit IV
aF: Photosystem I reaction center subunit III
aI: Photosystem I reaction center subunit VIII
aJ: Photosystem I reaction center subunit IX
aK: Photosystem I reaction center subunit PsaK 1
aL: Photosystem I reaction center subunit XI
aM: Photosystem I reaction center subunit XII
bA: Photosystem I P700 chlorophyll a apoprotein A1
bB: Photosystem I P700 chlorophyll a apoprotein A2
bC: Photosystem I iron-sulfur center
bD: Photosystem I reaction center subunit II, cyanelle
bE: Photosystem I reaction center subunit IV
bF: Photosystem I reaction center subunit III
bI: Photosystem I reaction center subunit VIII
bJ: Photosystem I reaction center subunit IX
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
cA: Photosystem I P700 chlorophyll a apoprotein A1
cB: Photosystem I P700 chlorophyll a apoprotein A2
cC: Photosystem I iron-sulfur center
cD: Photosystem I reaction center subunit II, cyanelle
cE: Photosystem I reaction center subunit IV
cF: Photosystem I reaction center subunit III
cI: Photosystem I reaction center subunit VIII
cJ: Photosystem I reaction center subunit IX
cK: Photosystem I reaction center subunit PsaK 1
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
dA: Photosystem I P700 chlorophyll a apoprotein A1
dB: Photosystem I P700 chlorophyll a apoprotein A2
dC: Photosystem I iron-sulfur center
dD: Photosystem I reaction center subunit II, cyanelle
dE: Photosystem I reaction center subunit IV
dF: Photosystem I reaction center subunit III
dI: Photosystem I reaction center subunit VIII
dJ: Photosystem I reaction center subunit IX
dL: Photosystem I reaction center subunit XI
dM: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,399,738480
Polymers1,047,32742
Non-polymers352,411438
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 8 molecules aAbAcAdAaBbBcBdB

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


Mass: 83397.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: A0A097PBL3, photosystem I
#2: Protein
Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82316.312 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48113, photosystem I

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Protein , 1 types, 4 molecules aCbCcCdC

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


Mass: 8850.221 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P31173, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 30 molecules aDbDcDdDaEbEcEdEaFbFcFdFaIbIcIdIaJbJcJdJaKcKaLbLcLdLaMbMcMdM

#4: Protein
Photosystem I reaction center subunit II, cyanelle / Photosystem I 20 kDa subunit / PSI-D


Mass: 23693.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: Q9T4W8
#5: Protein
Photosystem I reaction center subunit IV / PSI-E


Mass: 8058.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48114
#6: Protein
Photosystem I reaction center subunit III / PSI-F


Mass: 20697.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48115
#7: Protein/peptide
Photosystem I reaction center subunit VIII / PSI-I


Mass: 3772.620 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48116
#8: Protein/peptide
Photosystem I reaction center subunit IX / PSI-J


Mass: 4483.274 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48117
#9: Protein Photosystem I reaction center subunit PsaK 1


Mass: 15704.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote)
#10: Protein
Photosystem I reaction center subunit XI


Mass: 15376.591 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote)
#11: Protein/peptide
Photosystem I reaction center subunit XII / PSI-M


Mass: 3334.065 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanophora paradoxa (eukaryote) / References: UniProt: P48185

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Non-polymers , 7 types, 438 molecules

#12: Chemical
ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 326 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / 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: PSI tetramer / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Cyanophora paradoxa (eukaryote)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
150 mMMES-NaOH1
20.03 %DDM1
SpecimenConc.: 0.048 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4Gctf1.18CTF correction
7UCSF Chimera1.12model fitting
9PHENIX1.13_2998model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 723316
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40679 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient

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