[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

TitleMolecular and structural insights into neurosporene accumulation in Rhodobacter sphaeroides G1C.
Journal, issue, pagesPhotosynth. Res., Vol. 163, Page 53, Year 2025
Publish dateNov 14, 2024
AuthorsYu-Lu Wu / Guang-Lei Wang / Xiang-Ping Wang / Xing-Yu Yue / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Richard J Cogdell / Long-Jiang Yu /
PubMed AbstractCarotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid ...Carotenoids are tetraterpenoid pigments that play important roles in photosynthesis, provide protection from oxidative stress, and facilitate environmental adaptation. The green-colored carotenoid neurosporene, a key intermediate in carotenoid biosynthesis, plays a central role in the production of several other carotenoids; however, neurosporene accumulation is rare in nature. In this study, we investigated the accumulation of neurosporene in Rhodobacter sphaeroides strain G1C, a mutant derivative of wild-type Rba. sphaeroides 2.4.1 obtained by nitrosoguanidine mutagenesis. Whole-genome sequencing of strain G1C identified a nonsense mutation in the crtC gene resulting in enzyme inactivation and disruption of normal carotenoid biosynthesis. Physiological analysis and cryo-EM structural analysis of the major photosynthetic complexes of strain G1C showed that the accumulation of neurosporene did not significantly alter either the structure or functioning of the light-harvesting complexes and had no perceptible effect on photosynthetic growth. While the carotenoid composition of strain G1C shifts from spheroidene to neurosporene, its photocomplexes remain structurally intact and their physiological properties remain largely unchanged. This study provides genomic insights into the importance of CrtC activity to the production of carotenoids in Rba. sphaeroides and highlights the unexpected finding that carotenoid substitution in photocomplexes can occur without significantly disrupting photocomplex function.
External linksPhotosynth. Res. / PubMed:41114893
MethodsEM (single particle)
Resolution2.6 Å
Structure data

62409

9klm

EMDB-62409, PDB-9klm:
Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex
Method: EM (single particle) / Resolution: 2.6 Å

Chemicals

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

ChemComp-U10:
UBIQUINONE-10

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-FE:
Unknown entry

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

PDB-1ef2:
CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE

Source
  • cereibacter sphaeroides (bacteria)
KeywordsPHOTOSYNTHESIS / LH1-RC / Rhodobacter sphaeroides G1C / neurosporene

+
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