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- PDB-9eys: Structure of Far-Red Photosystem I from C. thermalis PCC 7203 -

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Entry
Database: PDB / ID: 9eys
TitleStructure of Far-Red Photosystem I from C. thermalis PCC 7203
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
  • Photosystem one PsaX
KeywordsPHOTOSYNTHESIS / Chlorophyll f / Photosystem I / Far-red / cyanobacteria
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
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 PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / 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 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 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 / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / 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 / 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 / Chlorophyll F / EICOSANE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chlorophyll F / EICOSANE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit XII / Photosystem one PsaX / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II
Similarity search - Component
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsConsoli, G. / Tufaill, F. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Citation
Journal: To Be Published
Title: Structure of Far-Red Photosystem I from C. thermalis PCC 7203
Authors: Consoli, G. / Tufail, F. / Leong, H. / Fantuzzi, A. / Rutherford, A.W.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Murray, J.W. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Murray, J.W. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 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
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: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
X: Photosystem one PsaX
N: Photosystem I P700 chlorophyll a apoprotein A1
O: Photosystem I P700 chlorophyll a apoprotein A2
P: Photosystem I iron-sulfur center
Q: Photosystem I reaction center subunit II
R: Photosystem I reaction center subunit IV
S: Photosystem I reaction center subunit III
T: Photosystem I reaction center subunit VIII
U: Photosystem I reaction center subunit IX
V: Photosystem I reaction center subunit PsaK
W: Photosystem I reaction center subunit XI
Y: Photosystem I reaction center subunit XII
Z: Photosystem one PsaX
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
g: Photosystem I reaction center subunit VIII
h: Photosystem I reaction center subunit IX
i: Photosystem I reaction center subunit PsaK
j: Photosystem I reaction center subunit XI
k: Photosystem I reaction center subunit XII
l: Photosystem one PsaX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,111,568438
Polymers796,99336
Non-polymers314,575402
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules ANaBOb

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


Mass: 86382.375 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TWJ0, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83304.703 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TVF3, photosystem I

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

#4: Protein Photosystem I reaction center subunit II


Mass: 15798.022 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_4755
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9U6S7
#5: Protein Photosystem I reaction center subunit IV


Mass: 7634.748 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TYF8
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17859.723 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TZX8
#7: Protein Photosystem I reaction center subunit VIII


Mass: 5879.917 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1016
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TVX2
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 5297.427 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TYS7
#9: Protein Photosystem I reaction center subunit PsaK


Mass: 8201.732 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TX25
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 19726.336 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TX29
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3540.284 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: psaM, Chro_0108
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TSY6

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Protein / Protein/peptide / Sugars , 3 types, 15 molecules CPcXZl

#12: Protein/peptide Photosystem one PsaX


Mass: 3199.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_0654
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TUG4
#20: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8839.232 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TVB5, photosystem I

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Non-polymers , 11 types, 798 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-F6C / Chlorophyll F / [methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium


Mass: 905.457 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 246 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#16: 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
#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE


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


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#21: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C45H86O10
#22: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H42
#23: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#24: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: Far Red Photosystem I / Type: COMPLEX
Details: Trimeric photosystem I from C. thermalis grown under far-red light condition.
Entity ID: #1-#12 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: C. thermalis (bacteria) / Strain: PCC 7203 / Cellular location: thylakoid membrane
Buffer solutionpH: 6.5
Details: 20 mM MES NaOH pH 6.5 5 mM CaCl2 5 mM MgCl2 0.03% betaDM
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the sample was monodisperse, but the concentration high
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8854

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1560000
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83138 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002479578
ELECTRON MICROSCOPYf_angle_d0.5515112080
ELECTRON MICROSCOPYf_chiral_restr0.04269780
ELECTRON MICROSCOPYf_plane_restr0.004214388
ELECTRON MICROSCOPYf_dihedral_angle_d16.878414169

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