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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 / electron transfer 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 / 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 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.
CitationJournal: 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

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Structure visualization

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  • Deposited structure unit
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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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