[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

TitleStructural basis for the assembly and energy transfer between the cyanobacterial PSI core and the double-layered IsiA proteins.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Page 592, Year 2025
Publish dateDec 20, 2025
AuthorsLong Si / Yingyue Zhang / Xiaodong Su / Xuelin Zhao / Xiaomin An / Lu-Ning Liu / Peng Cao / Mei Li /
PubMed AbstractIron-limitation is a common stress factor in natural environments. To survive under iron-starved conditions, cyanobacteria overexpress iron stress-induced protein A (IsiA), which is crucial for light- ...Iron-limitation is a common stress factor in natural environments. To survive under iron-starved conditions, cyanobacteria overexpress iron stress-induced protein A (IsiA), which is crucial for light-harvesting and photoprotection. Multiple IsiA proteins form a single- or double-layered architecture encircling the photosystem I (PSI) core, forming various PSI-IsiA supercomplexes. The assembly and energy transfer mechanisms of double-layered PSI-IsiA supercomplexes remain unelucidated. Here, we present high-resolution structures of two PSI-IsiA supercomplexes isolated from the cyanobacterium Thermosynechococcus elongatus BP-1 cultured under iron-starved conditions. The PSI-IsiA complex contains a trimeric PSI core surrounded by 43 IsiA subunits assembled into a closed double-ring. The PSI-IsiA complex contains 13 IsiA proteins arranged in a double-layered architecture attached to the monomeric PSI core. Atomic force microscopy demonstrates the presence and distribution of different PSI-IsiA complexes within native thylakoid membranes isolated from iron-starved cells. Our findings provide insights into the structural variability and adaptive mechanisms of PSI-IsiA complexes.
External linksNat Commun / PubMed:41422266 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 3.5 Å
Structure data

EMDB-63527, PDB-9lzj:
The PSI3-IsiA43 complex with a closed double ring of IsiA proteins bound to a trimeric PSI core
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-63528, PDB-9lzk:
The PSI1-IsiA13 complex with double-layered IsiA proteins bound to the monomeric PSI core
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-CLA:
CHLOROPHYLL A

ChemComp-PQN:
PHYLLOQUINONE

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-BCR:
BETA-CAROTENE

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

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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

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

ChemComp-CA:
Unknown entry

Source
  • thermosynechococcus vestitus bp-1 (bacteria)
KeywordsPHOTOSYNTHESIS / Photosystem-antenna Complex

+
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