[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 of giant kelp Photosystem I-FCP uncovers drivers of antenna evolution across the red lineage.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateMay 21, 2026
AuthorsJenevieve D Weissman / Pablo Maturana / Hui M O Oung / Reece Riddle / Gabrielle Wyatt / Viktoria G T Dubinin / Philipp Zerbe / María Maldonado /
PubMed AbstractBrown algae and other red-algae-derived organisms are major contributors to global CO fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtained the structure ...Brown algae and other red-algae-derived organisms are major contributors to global CO fixation via photosynthesis. To understand the photosynthetic function of brown algae, we obtained the structure of giant kelp Macrocystis pyrifera photosystem I (PSI) with a fucoxanthin-chlorophyll-protein (FCP) antenna and compared it to known structures from the red-algal lineage. We identified differences in M. pyrifera's antenna composition, architecture, and chlorophyll networks, as well as a pronounced variation in transmembrane hydrophobic thickness across the PSI-FCP supercomplex, with implications for photochemical function. Our work lays the foundation to understand kelp's high photosynthetic productivity and reveals drivers of antenna conservation and diversification for the red lineage.
External linksNat Commun / PubMed:42168190 / PubMed Central
MethodsEM (single particle)
Resolution2.47 - 5.21 Å
Structure data

EMDB-72805: Focused refinement of Macrocystis pyrifera PSI-FCP around PSI
Method: EM (single particle) / Resolution: 2.47 Å

EMDB-72806: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP1
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-72807: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP2
Method: EM (single particle) / Resolution: 4.71 Å

EMDB-72808: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP3
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-72809: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP4
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-72810: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP5
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-72811: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP6
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-72812: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP7
Method: EM (single particle) / Resolution: 3.11 Å

EMDB-72813: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP8
Method: EM (single particle) / Resolution: 2.97 Å

EMDB-72814: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP9
Method: EM (single particle) / Resolution: 3.78 Å

EMDB-72816: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP10
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-72817: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP11
Method: EM (single particle) / Resolution: 3.02 Å

EMDB-72818: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP13
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-72819: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP15
Method: EM (single particle) / Resolution: 4.71 Å

EMDB-72820: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP16
Method: EM (single particle) / Resolution: 4.81 Å

EMDB-72821: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP17
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-72822: Focused refinement of Macrocystis pyrifera PSI-FCP around FCP19
Method: EM (single particle) / Resolution: 4.92 Å

EMDB-72824: Focused refinement of Macrocystis pyrifera PSI-FCP around FCPB
Method: EM (single particle) / Resolution: 5.21 Å

EMDB-75351: Focused refinement of Macrocystis pyrifera PSI-FCP around FCPA
Method: EM (single particle) / Resolution: 3.97 Å

EMDB-76146: Composite map of Macrocystis pyrifera PSI-FCP supercomplex
Method: EM (single particle) / Resolution: 2.47 Å

EMDB-76202: Consensus map of Macrocystis pyrifera PSI-FCP supercomplex
Method: EM (single particle) / Resolution: 2.71 Å

Source
  • Macrocystis pyrifera (giant kelp)

+
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