[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

TitleThe architecture and energy transfer pathways of PSI-LHCI-LHCII in the phototrophic flagellate Euglena gracilis.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateMar 5, 2026
AuthorsGuoqiang Huang / Shishang Dong / Lin Li / Lixia Zhu / Jiayi Bai / Xing Han / Jiasheng Jiang / Jinxin Ju / Sen-Fang Sui / Xiaochun Qin /
PubMed AbstractPhotosystem I (PSI) harvests light through light-harvesting complexes (LHCs) to drive electron transfer. Euglena gracilis, a secondary endosymbiotic green alga, yet the architecture of its PSI-LHCs ...Photosystem I (PSI) harvests light through light-harvesting complexes (LHCs) to drive electron transfer. Euglena gracilis, a secondary endosymbiotic green alga, yet the architecture of its PSI-LHCs supercomplex has remained unresolved. Here, we report a 2.06 Å cryo-electron microscopy structure of the E. gracilis PSI-LHCI-LHCII supercomplex, revealing a minimal PSI core associated with ten antennas arranged in two layers on the PsaM-facing side. Each inner and outer LHC forms a face-to-face pair, while four LHCI heterodimers, stabilized by conserved Loop_23 motifs, assemble into two tetramers bridged by a central LHCI-LHCII pair. Notably, a ~ 40-residue insertion in PsaD was observed, anchoring LHC-3 and stabilizing LHC belts. Moreover, Euglena-specific chlorophylls and a distinctive arrangement of red chlorophylls establish a distinct pigment network, channeling excitation-energy into the core. These findings uncover a lineage-specific strategy for light-harvesting, highlighting how secondary plastids remodel PSI-LHCs architecture to support photosynthesis.
External linksNat Commun / PubMed:41786722 / PubMed Central
MethodsEM (single particle)
Resolution2.06 - 2.6 Å
Structure data

EMDB-65931: Cryo-EM consensus map of PSI-LHCI-LHCII supercomplex from Euglena gracilis
Method: EM (single particle) / Resolution: 2.06 Å

EMDB-65939: Cryo-EM focused refinement map of LHC-(6-9) from Euglena gracilis
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-65940: Cryo-EM focused refinement map of LHC-10 of the PSI-LHCI-LHCII supercomplex from Euglena gracilis
Method: EM (single particle) / Resolution: 2.57 Å

Source
  • Euglena gracilis (euglena)

+
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