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- PDB-9l0a: PSI trimer of Arthrospira platensis NIES-39 -

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Basic information

Entry
Database: PDB / ID: 9l0a
TitlePSI trimer of Arthrospira platensis NIES-39
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
  • Unknown
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homologyBETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand
Function and homology information
Biological speciesArthrospira platensis NIES-39 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsKato, K. / Nakajima, Y. / Shen, J.R. / Nagao, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for unique low-energy chlorophylls within photosystem I in Arthrospira platensis
Authors: Kato, K. / Nakajima, Y. / Shen, J.R. / Nagao, R.
History
DepositionDec 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data 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
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
K: Unknown
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem I reaction center subunit psaX
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
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
bK: Unknown
bL: Photosystem I reaction center subunit XI
bM: Photosystem I reaction center subunit XII
bX: Photosystem I reaction center subunit psaX
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
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: Unknown
cL: Photosystem I reaction center subunit XI
cM: Photosystem I reaction center subunit XII
cX: Photosystem I reaction center subunit psaX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,066,794414
Polymers775,29036
Non-polymers291,504378
Water6,323351
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, 6 molecules AbAcABbBcB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 83347.781 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 83483.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)

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Protein , 2 types, 6 molecules CbCcCKbKcK

#3: Protein Photosystem I iron-sulfur center


Mass: 8823.235 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#9: Protein Unknown


Mass: 6996.616 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)

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Photosystem I reaction center subunit ... , 8 types, 24 molecules DbDcDEbEcEFbFcFIbIcIJbJcJLbLcLMbMcMXbXcX

#4: Protein Photosystem I reaction center subunit II


Mass: 15863.099 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#5: Protein Photosystem I reaction center subunit IV


Mass: 8621.794 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#6: Protein Photosystem I reaction center subunit III


Mass: 17740.369 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4236.111 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4765.721 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#10: Protein Photosystem I reaction center subunit XI


Mass: 17018.334 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#11: Protein/peptide Photosystem I reaction center subunit XII


Mass: 3426.116 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)
#12: Protein/peptide Photosystem I reaction center subunit psaX


Mass: 4107.841 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arthrospira platensis NIES-39 (bacteria)

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Non-polymers , 10 types, 729 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 273 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 15 / Source method: obtained synthetically
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: PSI-trimer / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1.08 MDa / Experimental value: NO
Source (natural)Organism: Arthrospira platensis NIES-39 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESMES-NaOH1
20.03 %DDMDDM1
SpecimenConc.: 2.5 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13Servalcat0.2.95model refinement
14REFMAC5.8.0267model refinement
15PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4493216
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121244 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: experimental model

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