[English] 日本語
Yorodumi
- PDB-9l0k: Cryo-EM structure of PSI-11ACPIs from Rhodomonas sp. NIES-2332 at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l0k
TitleCryo-EM structure of PSI-11ACPIs from Rhodomonas sp. NIES-2332 at 2.14 angstrom resolution
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • ACPI-a
  • ACPI-b
  • ACPI-c
  • ACPI-d
  • ACPI-h
  • ACPI-i
  • ACPI-k
  • ACPI-l
  • ACPI-m
  • ACPI-n
  • ACPI-s
  • Photosystem I iron-sulfur center
  • PsaQ
  • PsaR
KeywordsPHOTOSYNTHESIS / photosynthesis complex
Function / homology
Function and homology information


CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / :
Similarity search - Component
Biological speciesRhodomonas sp. NIES-2332 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsZhang, W.Y. / Akita, F. / Shen, J.R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Front Plant Sci / Year: 2025
Title: Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga sp. NIES-2332.
Authors: Wenyue Zhang / Nozomi Yonehara / Mizuki Ishii / Haowei Jiang / Romain La Rocca / Pi-Cheng Tsai / Hongjie Li / Koji Kato / Fusamichi Akita / Jian-Ren Shen
Abstract: Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte ...Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte alga whose LHCs contain unique chlorophyll proteins (ACPs) and phycobiliproteins. We purified PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte sp. NIES-2332 and analyzed their structures at high resolutions of 2.08 Å and 2.17 Å, respectively, using cryo-electron microscopy. These structures are largely similar to those reported previously from two other species of cryptophytes, but exhibited some differences in both the pigment locations and subunit structures. A part of the antenna subunits of both photosystems is shifted compared with the previously reported structures from other species of cryptophytes, suggesting some differences in the energy transfer rates from the antenna to the PSI and PSII cores. Newly identified lipids are found to occupy the interfaces between the antennae and cores, which may be important for assembly and stabilization of the supercomplexes. Water molecules surrounding three iron-sulfur clusters of the PSI core are found in our high-resolution structure, some of which are conserved from cyanobacteria to higher plants but some are different. In addition, our structure of PSII-ACPII lacks the subunits of oxygen-evolving complex as well as the MnCaO cluster, suggesting that the cells are in the S-growth phase, yet the PSI-ACPI structure showed the binding of PsaQ, suggesting that it is in an L-phase. These results suggest that the S-phase and L-phase can co-exist in the cryptophytic cells. The high-resolution structures of both PSI-ACPIs and PSII-ACPIIs solved in this study provide a more solid structural basis for elucidating the energy transfer and quenching mechanisms in this group of the organisms.
History
DepositionDec 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _em_admin.last_update
Revision 1.1Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
K: Photosystem I reaction center subunit PsaK
s: ACPI-s
c: ACPI-c
a: ACPI-a
b: ACPI-b
h: ACPI-h
m: ACPI-m
l: ACPI-l
k: ACPI-k
i: ACPI-i
j: ACPI-m
d: ACPI-d
R: PsaR
n: ACPI-n
Q: PsaQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,362379
Polymers576,18425
Non-polymers276,179354
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 83441.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 82087.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

-
Protein , 14 types, 15 molecules CscabhmjlkidRnQ

#3: Protein Photosystem I iron-sulfur center


Mass: 8759.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#12: Protein ACPI-s


Mass: 31529.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#13: Protein ACPI-c


Mass: 23785.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#14: Protein ACPI-a


Mass: 23380.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#15: Protein ACPI-b


Mass: 24814.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#16: Protein ACPI-h


Mass: 23646.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#17: Protein ACPI-m


Mass: 22379.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#18: Protein ACPI-l


Mass: 18985.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#19: Protein ACPI-k


Mass: 24658.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#20: Protein ACPI-i


Mass: 21402.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#21: Protein ACPI-d


Mass: 23069.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#22: Protein PsaR


Mass: 13949.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#23: Protein ACPI-n


Mass: 23069.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#24: Protein PsaQ


Mass: 23676.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

-
Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLMK

#4: Protein Photosystem I reaction center subunit II


Mass: 15585.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#5: Protein Photosystem I reaction center subunit IV


Mass: 7309.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#6: Protein Photosystem I reaction center subunit III


Mass: 20849.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3927.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4974.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#9: Protein Photosystem I reaction center subunit XI


Mass: 16489.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#10: Protein/peptide Photosystem I reaction center subunit XII


Mass: 3318.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#11: Protein Photosystem I reaction center subunit PsaK


Mass: 8715.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

-
Sugars , 2 types, 7 molecules

#30: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#33: 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

-
Non-polymers , 12 types, 758 molecules

#25: 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
#26: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#27: 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
#28: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#29: Chemical...
ChemComp-WVN / 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene / ALPHA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#31: 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
#32: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#35: 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.: 45 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#37: 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.: 8 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Photosystem I complex binding with 11 ACPIs / Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 0.726968 MDa / Experimental value: NO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33179 / Symmetry type: POINT
RefinementHighest resolution: 2.14 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more