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- PDB-9vfj: PSI-LHCI of Euglena gracilis strain Z -

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Basic information

Entry
Database: PDB / ID: 9vfj
TitlePSI-LHCI of Euglena gracilis strain Z
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • Chloroplast light-harvesting complex I protein
  • LHCI-1
  • LHCI-10
  • LHCI-11
  • LHCI-2
  • LHCI-3
  • LHCI-4
  • LHCI-6
  • LHCI-7
  • LHCI-8
  • LHCI-9
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosynthesis, light harvesting / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / membrane
Similarity search - Function
Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC ...Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 / 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 / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chloroplast light-harvesting complex I protein ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chloroplast light-harvesting complex I protein / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsKato, K. / Nakajima, Y. / Shen, J.R. / Nagao, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K14211, JP22H04916, and JP23H02423 Japan
CitationJournal: To Be Published
Title: Structure of a divergent photosystem I supercomplex from Euglena gracilis outside green and red lineages
Authors: Kato, K. / Nakajima, Y. / Sakamoto, R. / Kumazawa, M. / Ifuku, K. / Shen, J.R. / Takabayashi, A. / Nagao, R.
History
DepositionJun 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 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
J: Photosystem I reaction center subunit IX
M: Photosystem I reaction center subunit XII
1: LHCI-1
2: LHCI-2
3: LHCI-3
4: LHCI-4
5: Chloroplast light-harvesting complex I protein
6: LHCI-6
7: LHCI-7
8: LHCI-8
9: LHCI-9
10: LHCI-10
11: LHCI-11
12: LHCI-11
13: LHCI-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,551,344363
Polymers1,302,27921
Non-polymers249,065342
Water79344
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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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 85183.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82780.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P19431, photosystem I

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Protein , 12 types, 14 molecules C12345678910111213

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


Mass: 8784.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P31556, photosystem I
#9: Protein LHCI-1


Mass: 52475.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#10: Protein LHCI-2


Mass: 65361.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein LHCI-3


Mass: 46443.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#12: Protein LHCI-4


Mass: 44705.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#13: Protein Chloroplast light-harvesting complex I protein


Mass: 27130.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: A8HPE4
#14: Protein LHCI-6


Mass: 95660.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#15: Protein LHCI-7


Mass: 66506.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#16: Protein LHCI-8


Mass: 89149.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#17: Protein LHCI-9


Mass: 94434.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#18: Protein LHCI-10


Mass: 69436.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#19: Protein LHCI-11


Mass: 112373.086 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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

#4: Protein Photosystem I reaction center subunit II


Mass: 76196.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: Protein Photosystem I reaction center subunit IV


Mass: 17927.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#6: Protein Photosystem I reaction center subunit III


Mass: 35240.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#7: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4298.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P30394
#8: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3445.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: P31479

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Sugars , 1 types, 1 molecules

#27: 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, 385 molecules

#20: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 236 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#22: 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
#23: 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
#24: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 42 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: PSI-LHCI / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Euglena gracilis (euglena)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 mMMES1
20.03 %Sucrose monolaurate1
SpecimenConc.: 2.5 mg/ml / Embedding 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 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.16model fitting
9Servalcat0.4.32model refinement
10REFMAC5.8.0419model refinement
11PHENIX1.20.1model refinement
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 507565
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56060 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: experimental model

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