[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 and quantum chemical basis for OCP-mediated quenching of phycobilisomes.
Journal, issue, pagesSci Adv, Vol. 10, Issue 14, Page eadk7535, Year 2024
Publish dateApr 5, 2024
AuthorsPaul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld /
PubMed AbstractCyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
External linksSci Adv / PubMed:38578996 / PubMed Central
MethodsEM (single particle)
Resolution1.63 - 2.2 Å
Structure data

41434

8to2

EMDB-41434, PDB-8to2:
Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Method: EM (single particle) / Resolution: 2.0 Å

41435

8to5

EMDB-41435, PDB-8to5:
Central rod disk in C1 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)
Method: EM (single particle) / Resolution: 1.87 Å

EMDB-41436: Central rod disk in D3 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)
Method: EM (single particle) / Resolution: 1.63 Å

EMDB-41463: Synechocystis PCC 6803 Phycobilisome quenched by OCP, high resolution
Method: EM (single particle) / Resolution: 2.2 Å

41475

8tpj

EMDB-41475, PDB-8tpj:
Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)
Method: EM (single particle) / Resolution: 2.1 Å

41585

8tro

EMDB-41585, PDB-8tro:
Rod from high-resolution phycobilisome quenched by OCP (local refinement)
Method: EM (single particle) / Resolution: 1.9 Å

Chemicals

ChemComp-CYC:
PHYCOCYANOBILIN

ChemComp-45D:
beta,beta-carotene-4,4'-dione

ChemComp-HOH:
WATER

Source
  • Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
  • synechocystis sp. pcc 6803 (bacteria)
KeywordsPHOTOSYNTHESIS / Complex / light harvesting / pigment

+
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