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- PDB-10eg: Thermosynechococcus vestitus (BP-1) Photosystem I Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 10eg
TitleThermosynechococcus vestitus (BP-1) Photosystem I Complexed with Platinum Nanoparticles
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Nanoparticles / Biohybrid / Photosystem
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsEmerson, M.D. / Gisriel, C.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Biorxiv / Year: 2026
Title: Molecular design principles for Photosystem I-based biohybrid solar fuel catalysts.
Authors: Emerson, M.D. / Damaraju, S.N.S. / Short, A.H. / Alvord, Z.B. / Palmer, Z.A. / Mehra, H.S. / Brininger, C.M. / Vermaas, J.V. / Utschig, L.M. / Gisriel, C.J.
History
DepositionJan 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
G: Photosystem I P700 chlorophyll a apoprotein A1
a: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
H: Photosystem I P700 chlorophyll a apoprotein A2
b: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
N: Photosystem I iron-sulfur center
c: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
O: Photosystem I reaction center subunit II
d: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
P: Photosystem I reaction center subunit IV
e: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
Q: Photosystem I reaction center subunit III
f: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
R: Photosystem I reaction center subunit VIII
i: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
S: Photosystem I reaction center subunit IX
j: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
T: Photosystem I reaction center subunit PsaK
k: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
U: Photosystem I reaction center subunit XI
l: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
V: Photosystem I reaction center subunit XII
m: Photosystem I reaction center subunit XII
W: Photosystem I 4.8K protein
X: Photosystem I 4.8K protein
x: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,080,636417
Polymers775,18936
Non-polymers305,447381
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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Photosystem I ... , 12 types, 36 molecules AGaBHbCNcDOdEPeFQfIRiJSjKTkLUl...

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


Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17716.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4297.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4770.698 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16287.765 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein


Mass: 4424.317 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DKP6

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Non-polymers , 8 types, 381 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


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


Mass: 893.489 Da / Num. of mol.: 285 / 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
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#19: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#20: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: Thermosynechococcus vestitus (BP-1) Photosystem I Complexed with Platinum Nanoparticles
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 0.934541 MDa / Experimental value: NO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Buffer solutionpH: 7.4
Buffer componentConc.: 20 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenEmbedding 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: 277.5 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: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.13 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 906919
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19151 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01275795
ELECTRON MICROSCOPYf_angle_d2.175107616
ELECTRON MICROSCOPYf_dihedral_angle_d30.43218300
ELECTRON MICROSCOPYf_chiral_restr0.0869486
ELECTRON MICROSCOPYf_plane_restr0.01612909

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