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- PDB-9gbi: Cryo-EM structure of Arabidopsis thaliana PSI-LHCI wild-type -

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Basic information

Entry
Database: PDB / ID: 9gbi
TitleCryo-EM structure of Arabidopsis thaliana PSI-LHCI wild-type
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I chlorophyll a/b-binding protein ...) x 2
  • (Photosystem I reaction center subunit ...) x 10
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / PSI-LHCI / Arabidopsis thaliana / light harvesting / far-red absorption
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast membrane / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / mitochondrion / extracellular region / metal ion binding / nucleus / cytosol
Similarity search - Function
Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic ...Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 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 PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 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 B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein 4, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit IV B, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsCapaldi, S. / Chaves-Sanjuan, A. / Bonnet, D.M.V. / Bassi, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101053983-GrInSunEuropean Union
CitationJournal: To Be Published
Title: Structural determinants for red-shifted absorption in higher-plants Photosystem I
Authors: Capaldi, S. / Guardini, Z. / Montepietra, D. / Pagliuca, V.F. / Amelii, A. / Bonnet, D.M.V. / Chaves-Sanjuan, A. / Dall'Osto, L. / Bassi, R.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 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

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein 6, chloroplastic
2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
4: Chlorophyll a-b binding protein 4, chloroplastic
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-2, chloroplastic
E: Photosystem I reaction center subunit IV B, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI-1, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI, chloroplastic
K: Photosystem I reaction center subunit psaK, chloroplastic
N: Photosystem I reaction center subunit N, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)550,561227
Polymers380,42217
Non-polymers170,140210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 14

#1: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 22522.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667
#4: Protein Chlorophyll a-b binding protein 4, chloroplastic / LHCI type III CAB-4


Mass: 22274.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P27521

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Photosystem I chlorophyll a/b-binding protein ... , 2 types, 2 molecules 23

#2: Protein Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / Lhca2 / LHCI type III LHCA2


Mass: 23448.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8
#3: Protein Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Lhca3*1 / LHCI type III LHCA3


Mass: 25234.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#5: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 83180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A8F5S1X0, photosystem I
#6: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82448.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A8F5P166, photosystem I

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Protein , 1 types, 1 molecules C

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


Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I

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Photosystem I reaction center subunit ... , 10 types, 10 molecules DEFGHIJLKN

#8: Protein Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I 20 kDa subunit 2 / PSI-D2


Mass: 17684.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56
#9: Protein Photosystem I reaction center subunit IV B, chloroplastic / PSI-E B


Mass: 10561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S714
#10: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17319.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8
#11: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 11000.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7
#12: Protein Photosystem I reaction center subunit VI-1, chloroplastic / PSI-H1


Mass: 10366.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI7
#13: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4137.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56768
#14: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 5021.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A8F5NZW2
#15: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 17982.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4
#16: Protein Photosystem I reaction center subunit psaK, chloroplastic / PSI-K / Photosystem I subunit X


Mass: 8468.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5
#17: Protein Photosystem I reaction center subunit N, chloroplastic / PSI-N


Mass: 9720.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P49107

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Sugars , 2 types, 4 molecules

#25: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#28: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 9 types, 206 molecules

#18: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 143 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#26: 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 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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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: Photosystem I supercomplex (PSI-LHCI) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES1
20.05 %n-Dodecyl-Beta-Maltoside1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPU2.8image acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 575271
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54155 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7DKZ

7dkz


Accession code: 7DKZ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002138155
ELECTRON MICROSCOPYf_angle_d0.512754267
ELECTRON MICROSCOPYf_chiral_restr0.07334732
ELECTRON MICROSCOPYf_plane_restr0.00955866
ELECTRON MICROSCOPYf_dihedral_angle_d19.90038803

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