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Entry
Database: PDB / ID: 7qco
TitleThe structure of Photosystem I tetramer from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / cyanobacterium Chroococcidiopsis sp. TS-821
Function / homology
Function and homology information


thylakoid membrane / photosystem I reaction center / : / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...thylakoid membrane / photosystem I reaction center / : / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding
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 reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI ...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 / 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 / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / 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 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / PSI-F ...BETA-CAROTENE / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / PSI-F / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI
Similarity search - Component
Biological speciesChroococcidiopsis sp. TS-821 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSemchonok, D.A. / Mondal, J. / Cooper, J.C. / Schlum, K. / Li, M. / Amin, M. / Sorzano, C.O.S. / Ramirez-Aportela, E. / Kastritis, P.L. / Boekema, E.J. ...Semchonok, D.A. / Mondal, J. / Cooper, J.C. / Schlum, K. / Li, M. / Amin, M. / Sorzano, C.O.S. / Ramirez-Aportela, E. / Kastritis, P.L. / Boekema, E.J. / Guskov, A. / Bruce, B.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-0801470 United States
National Science Foundation (NSF, United States)EPS-1004083 United States
National Science Foundation (NSF, United States)2017219379 United States
Citation
Journal: Plant Commun / Year: 2022
Title: Cryo-EM structure of a tetrameric photosystem I from TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.
Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / ...Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / Albert Guskov / Barry D Bruce /
Abstract: Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric ...Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.
#1: Journal: Plant Commun / Year: 2022
Title: Cryo-EM structure of a tetrameric photosystem I from TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.
Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / ...Authors: Dmitry A Semchonok / Jyotirmoy Mondal / Connor J Cooper / Katrina Schlum / Meng Li / Muhamed Amin / Carlos O S Sorzano / Erney Ramírez-Aportela / Panagiotis L Kastritis / Egbert J Boekema / Albert Guskov / Barry D Bruce /
Abstract: Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric ...Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.
History
DepositionNov 24, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionApr 6, 2022ID: 6QWJ
Revision 1.0Apr 6, 2022Provider: 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
V: 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
E: Photosystem I P700 chlorophyll a apoprotein A1
G: Photosystem I P700 chlorophyll a apoprotein A2
H: Photosystem I iron-sulfur center
N: Photosystem I reaction center subunit II
W: Photosystem I reaction center subunit IV
O: Photosystem I reaction center subunit III
P: Photosystem I reaction center subunit VIII
Q: Photosystem I reaction center subunit IX
R: Photosystem I reaction center subunit PsaK
S: Photosystem I reaction center subunit XI
T: Photosystem I reaction center subunit XII
e: Photosystem I P700 chlorophyll a apoprotein A1
g: Photosystem I P700 chlorophyll a apoprotein A2
h: Photosystem I iron-sulfur center
n: Photosystem I reaction center subunit II
v: Photosystem I reaction center subunit IV
o: Photosystem I reaction center subunit III
p: Photosystem I reaction center subunit VIII
q: Photosystem I reaction center subunit IX
r: Photosystem I reaction center subunit PsaK
s: Photosystem I reaction center subunit XI
t: Photosystem I reaction center subunit XII
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
w: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,441,058506
Polymers1,066,98044
Non-polymers374,079462
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 8 molecules AEeaBGgb

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


Mass: 83352.641 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VGM5, photosystem I
#2: Protein
Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 82656.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VGS2, photosystem I

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Protein , 1 types, 4 molecules CHhc

#3: Protein
Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8939.309 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VD54, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 32 molecules DNndVWvwFOofIPpiJQqjKRrkLSslMTtm

#4: Protein
Photosystem I reaction center subunit II /


Mass: 18520.025 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VI21
#5: Protein
Photosystem I reaction center subunit IV /


Mass: 13551.099 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VHU0
#6: Protein
Photosystem I reaction center subunit III /


Mass: 18131.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VDZ1
#7: Protein/peptide
Photosystem I reaction center subunit VIII /


Mass: 4194.028 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6VDT4
#8: Protein/peptide
Photosystem I reaction center subunit IX /


Mass: 5760.832 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: BCR is not the part of the protein sequence / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: V5JYA2
#9: Protein
Photosystem I reaction center subunit PsaK /


Mass: 9753.610 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: CLA is not the part of the protein sequence / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6V467
#10: Protein
Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 18503.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: V5JYE0
#11: Protein/peptide
Photosystem I reaction center subunit XII / / PSI-M


Mass: 3382.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chroococcidiopsis sp. TS-821 (bacteria) / References: UniProt: A0A2S6V6A8

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Non-polymers , 5 types, 462 molecules

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


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 359 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 78 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN

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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: Photosystem I / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: YES
Source (natural)Organism: Chroococcidiopsis sp. TS-821 (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMMESC6H13NO4S1
210 mMmagnesium chlorideMgCl21
35 mMcalcium chlorideCaCl21
40.01 %DDMC24H46O111
SpecimenConc.: 0.32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 4.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4845
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 24

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4CTFFIND4CTF correctiongrigoriefflab
7Coot0.8.9.1model fitting
9PHENIX1.14model refinement
10Scipion2initial Euler assignmentxmipp3 - ransac
11Scipion2final Euler assignmenthighres
12Scipion2final Euler assignmentrelion 3.0
13Scipion2classificationrelion - 3D classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3243
Details: 325648 particles were selected from 4845 micrograph movies
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66130 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1JB0

1jb0

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00795562
ELECTRON MICROSCOPYf_angle_d0.802136131
ELECTRON MICROSCOPYf_dihedral_angle_d14.48745509
ELECTRON MICROSCOPYf_chiral_restr0.0511785
ELECTRON MICROSCOPYf_plane_restr0.00617777

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