[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructure and function of a huge photosystem I-fucoxanthin chlorophyll supercomplex from a coccolithophore.
Journal, issue, pagesScience, Vol. 389, Issue 6765, Page eadv2132, Year 2025
Publish dateSep 11, 2025
AuthorsLili Shen / Fei Ren / Yin-Chu Wang / Zhenhua Li / Mengyuan Zheng / Xiaoyi Li / Wenzheng Fan / Yanyan Yang / Min Sang / Cheng Liu / Guangye Han / Song Qin / Jianhua Fan / Lijin Tian / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
PubMed AbstractPhotosystem I (PSI) is a pigment-protein complex, which converts light energy into chemical energy in photosynthesis. Among photosynthetic organisms, PSI-LHC (light-harvesting complex) structures ...Photosystem I (PSI) is a pigment-protein complex, which converts light energy into chemical energy in photosynthesis. Among photosynthetic organisms, PSI-LHC (light-harvesting complex) structures exhibit substantial differences in their sizes, reflecting adaptation to different light environments. Here we report the structure of a PSI-fucoxanthin chlorophyll a/c binding protein (FCPI) supercomplex from the coccolithophore (Eh) at 2.79-angstrom resolution by cryo-electron microscopy, which showed a huge Eh-PSI-FCPI supercomplex containing 38 peripheral Eh-FCPI antennae and a linker protein (EhLP) in addition to the PSI core. A network of 819 pigments was found in Eh-PSI-FCPI, which functions to capture and transfer light energy with 95% quantum efficiency. This elucidates how its modular Eh-FCPI arrangement contributes to the expansion of PSI cross section and efficient light harvesting.
External linksScience / PubMed:40934304
MethodsEM (single particle)
Resolution2.79 Å
Structure data

61519

9jj8

EMDB-61519, PDB-9jj8:
Structural insights into the PSI-FCPI supercomplex from the coccolithophore Emiliania huxleyi
Method: EM (single particle) / Resolution: 2.79 Å

Chemicals

ChemComp-CLA:
CHLOROPHYLL A

ChemComp-PQN:
PHYLLOQUINONE

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

ChemComp-BCR:
BETA-CAROTENE

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

ChemComp-A86:
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-

ChemComp-KC2:
Chlorophyll c2

PDB-1eb1:
Complex structure of human thrombin with N-methyl-arginine inhibitor

PDB-1ecv:
CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH 5-IODO-2-(OXALYL-AMINO)-BENZOIC ACID

PDB-1eb4:
Histidine Ammonia-Lyase (HAL) Mutant F329A from Pseudomonas putida

Source
  • emiliania huxleyi ccmp1516 (eukaryote)
KeywordsPHOTOSYNTHESIS / PSI-FCPI supercomplex

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more