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- PDB-8zwb: 1.8 A resolution structure of the Photosystem I assembly intermed... -

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Basic information

Entry
Database: PDB / ID: 8zwb
Title1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits.
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
KeywordsPHOTOSYNTHESIS / PSI / assembly intermediates / photosystem I / biochemistry / cryo-EM / photosystem biogenesis.
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / plasma membrane
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaB / Photosystem I PsaA / 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
Similarity search - Domain/homology
: / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 ...: / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.83 Å
AuthorsNaschberger, A. / Komenda, J.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic24-10227S Czech Republic
European Research Council (ERC)854126European Union
CitationJournal: To Be Published
Title: 1.8 A resolution structure of the Photosystem I assembly intermediate lacking stromal subunits
Authors: Charras, Q. / Gupta, S. / Tichy, M. / Al-Amoudi, A. / Lukes, M. / Konik, P. / Sobotka, R. / Novak, P. / Komenda, J. / Naschberger, A.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 1
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,895155
Polymers203,6547
Non-polymers112,242148
Water6,395355
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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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

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


Mass: 83036.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: P29254, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81369.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: P29255, photosystem I

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Photosystem I reaction center subunit ... , 5 types, 5 molecules FIJKM

#3: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 18267.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: P29256
#4: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4414.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: Q55330
#5: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4535.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: Q55329
#6: Protein Photosystem I reaction center subunit PsaK 1 / Photosystem I subunit X 1


Mass: 8649.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: P72712
#7: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3382.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis (bacteria) / References: UniProt: P72986

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Sugars , 1 types, 26 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 11 types, 477 molecules

#8: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#9: 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
#10: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#11: 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
#12: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H56
#13: Chemical
ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H54O
#14: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#17: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-5X6 / Zeaxanthin / (1R)-4-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4R)-4-hydroxy-2,6,6-trimethylcyclohexen-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: Assembly Intermediate of Photosystem I lacking the cytosolic subunits PsaC, PsaD, and PsaE and the transmembrane subunit PsaL.
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Synechocystis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 1900 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333941 / Symmetry type: POINT

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