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- PDB-9wyp: The PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea -

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Basic information

Entry
Database: PDB / ID: 9wyp
TitleThe PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • ACPI-1
  • ACPI-11
  • ACPI-12
  • ACPI-13/10
  • ACPI-14
  • ACPI-2
  • ACPI-3
  • ACPI-4
  • ACPI-5
  • ACPI-6
  • ACPI-7
  • ACPI-8
  • ACPI-9
  • CCPI-S
  • Photosystem I iron-sulfur center
  • PsaO
  • PsaQ
  • PsaR
KeywordsPHOTOSYNTHESIS / STRUCTURAL PROTEIN
Function / homology
Function and homology information


plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis ...plastid thylakoid membrane / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / 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 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 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 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 / 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
Chem-8CT / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chem-II3 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...Chem-8CT / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chem-II3 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesChroomonas placoidea (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsLi, X.Y. / Mao, Z.Y. / Han, G.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA0911900 China
CitationJournal: Photosynth Res / Year: 2025
Title: Structural insights into a PSI-ACPI supercomplex from a cryptophyte alga Chroomonas placoidea.
Authors: Xingyue Li / Zhiyuan Mao / Zhenhua Li / Liangliang Shen / Xiaoyi Li / Yanyan Yang / Wenda Wang / Tingyun Kuang / Jian-Ren Shen / Guangye Han /
History
DepositionSep 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data 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
1: ACPI-1
2: ACPI-2
3: ACPI-3
4: ACPI-4
5: ACPI-5
6: ACPI-6
7: ACPI-7
8: ACPI-8
9: ACPI-12
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
O: PsaO
R: PsaR
Z: CCPI-S
a: ACPI-13/10
b: ACPI-14
c: ACPI-9
d: ACPI-13/10
e: ACPI-11
X: PsaQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,005,737458
Polymers671,30529
Non-polymers334,432429
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 , 18 types, 19 molecules 123456789CORZadbceX

#1: Protein ACPI-1


Mass: 23479.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#2: Protein ACPI-2


Mass: 23400.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#3: Protein ACPI-3


Mass: 24853.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#4: Protein ACPI-4


Mass: 23548.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#5: Protein ACPI-5


Mass: 24055.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#6: Protein ACPI-6


Mass: 22688.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#7: Protein ACPI-7


Mass: 24550.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#8: Protein ACPI-8


Mass: 23700.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#9: Protein ACPI-12


Mass: 23223.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#12: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8743.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI25, photosystem I
#21: Protein PsaO


Mass: 16384.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#22: Protein PsaR


Mass: 14468.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#23: Protein CCPI-S


Mass: 29319.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#24: Protein ACPI-13/10


Mass: 22270.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#25: Protein ACPI-14


Mass: 23755.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#26: Protein ACPI-9


Mass: 27212.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#27: Protein ACPI-11


Mass: 22451.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#28: Protein PsaQ


Mass: 24466.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)

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

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


Mass: 83493.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIB4, photosystem I
#11: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82219.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI95, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM

#13: Protein Photosystem I reaction center subunit II


Mass: 15590.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIA6
#14: Protein Photosystem I reaction center subunit IV


Mass: 7352.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AIF3
#15: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 20393.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI52
#16: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3975.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI78
#17: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4862.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI55
#18: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 8836.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI34
#19: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16490.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI68
#20: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3247.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote) / References: UniProt: A0A222AI28

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Sugars , 1 types, 2 molecules

#38: 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 , 11 types, 427 molecules

#29: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 255 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical...
ChemComp-II0 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol / Alloxanthin


Mass: 564.840 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical
ChemComp-II3 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Monadoxanthin


Mass: 566.856 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H54O2 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-IHT / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Allobetaxanthin


Mass: 550.856 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#35: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#36: 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.: 7 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#37: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#40: 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

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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: Structure of PSI-ACPI supercomplex from cryptophyte algae
Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL
Source (natural)Organism: Chroomonas placoidea (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: TFS 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 software
IDNameCategory
1crYOLOparticle selection
2Topazparticle selection
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171764 / Symmetry type: POINT
RefinementHighest resolution: 2.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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