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- PDB-8zob: Structure of the wild-type PSI-5VCPI supercomplex in Nannochlorop... -

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Basic information

Entry
Database: PDB / ID: 8zob
TitleStructure of the wild-type PSI-5VCPI supercomplex in Nannochloropsis oceanica
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • PSI subunit V
  • Photosystem I iron-sulfur center
  • PsaM
  • PsaS
  • VCPI-1
  • VCPI-2
  • VCPI-3
  • VCPI-4
  • VCPI-5
KeywordsPHOTOSYNTHESIS / PSI-VCPI supercomplex
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
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 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD ...: / : / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I reaction center subunit III / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / PSI subunit V
Similarity search - Component
Biological speciesNannochloropsis oceanica strain IMET1 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsShen, L.L. / Li, Z.H. / Shen, J.R. / Wang, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structure of the wild-type PSI-5VCPI supercomplex in Nannochloropsis oceanica
Authors: Shen, L.L. / Li, Z.H. / Shen, J.R. / Wang, W.D.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 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
5: VCPI-5
4: VCPI-4
3: VCPI-3
2: VCPI-2
1: VCPI-1
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
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
l: PSI subunit V
m: PsaM
g: PsaS
c: Photosystem I iron-sulfur center
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,814223
Polymers371,59516
Non-polymers167,219207
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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Protein , 8 types, 8 molecules 54321lgc

#1: Protein VCPI-5


Mass: 25849.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#2: Protein VCPI-4


Mass: 21611.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#3: Protein VCPI-3


Mass: 23046.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#4: Protein VCPI-2


Mass: 23865.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#5: Protein VCPI-1


Mass: 22652.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#13: Protein PSI subunit V


Mass: 18695.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJZ1
#15: Protein PsaS


Mass: 4698.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#16: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8763.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJY1, photosystem I

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

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


Mass: 82797.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJP7, photosystem I
#7: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82864.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RIQ1, photosystem I

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Photosystem I reaction center subunit ... , 5 types, 5 molecules defij

#8: Protein Photosystem I reaction center subunit II


Mass: 15037.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RIT2
#9: Protein Photosystem I reaction center subunit IV / Photosystem I subunit IV


Mass: 7668.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJT6
#10: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20813.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJ05
#11: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 5226.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJ07
#12: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4762.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
References: UniProt: T1RJW8

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Protein/peptide / Sugars , 2 types, 3 molecules m

#14: Protein/peptide PsaM


Mass: 3241.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nannochloropsis oceanica strain IMET1 (eukaryote)
#21: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 10 types, 205 molecules

#17: 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.: 21 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-A1L1G / (1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol


Mass: 616.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O5 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 146 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#22: 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
#23: Chemical ChemComp-A1L1F / [(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate


Mass: 785.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H72O7 / Feature type: SUBJECT OF INVESTIGATION
#24: 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
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C40H56 / 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: WT-PSI-5VCPI / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Nannochloropsis oceanica strain IMET1 (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66059 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00346270
ELECTRON MICROSCOPYf_angle_d1.03666199
ELECTRON MICROSCOPYf_dihedral_angle_d19.3727901
ELECTRON MICROSCOPYf_chiral_restr0.1395865
ELECTRON MICROSCOPYf_plane_restr0.0058724

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