[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

TitleCryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea.
Journal, issue, pagesNat Struct Mol Biol, Year 2025
Publish dateJan 24, 2025
AuthorsBianca Introini / Alexander Hahn / Werner Kühlbrandt /
PubMed AbstractThe nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to ...The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to plastoquinone while transporting H across the chloroplast membrane. This process boosts adenosine triphosphate production, regardless of NADPH levels. In flowering plants, NDH forms a supercomplex with photosystem I, enhancing its stability under high light. We report the cryo-electron microscopy structure of the NDH supercomplex in Spinacia oleracea at a resolution of 3.0-3.3 Å. The supercomplex consists of 41 protein subunits, 154 chlorophylls and 38 carotenoids. Subunit interactions are reinforced by 46 distinct lipids. The structure of NDH resembles that of mitochondrial complex I closely, including the quinol-binding site and an extensive internal aqueous passage for proton translocation. A well-resolved catalytic plastoquinone (PQ) occupies the PQ channel. The pronounced structural similarity to complex I sheds light on electron transfer and proton translocation within the NDH supercomplex.
External linksNat Struct Mol Biol / PubMed:39856350
MethodsEM (single particle)
Resolution3.09 - 3.34 Å
Structure data

EMDB-19241: NDH-PSI-LHCI supercomplex from S. oleracea: local refined peripheral arm of NDH
Method: EM (single particle) / Resolution: 3.27 Å

EMDB-19244: NDH-PSI-LHCI supercomplex from S. oleracea
Method: EM (single particle) / Resolution: 3.34 Å

EMDB-19246: NDH-PSI-LHCI supercomplex from S. oleracea: local refined membrane arm of NDH
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-19247: NDH-PSI-LHCI supercomplex from S. oleracea: local refined border region between NDH and PSI-LHCI-2
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-19248: NDH-PSI-LHCI supercomplex from S. oleracea: local refined PSI-LHCI-2
Method: EM (single particle) / Resolution: 3.09 Å

51527

9grx

EMDB-51527: NDH-PSI-LHCI supercomplex from S. oleracea: composite map
PDB-9grx: NDH-PSI-LHCI supercomplex from S. oleracea
Method: EM (single particle) / Resolution: 3.19 Å

Chemicals

ChemComp-BCR:
BETA-CAROTENE

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

PDB-1h1m:
CRYSTAL STRUCTURE OF QUERCETIN 2,3-DIOXYGENASE ANAEROBICALLY COMPLEXED WITH THE SUBSTRATE KAEMPFEROL

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

ChemComp-PQ9:
5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE

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

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-CLA:
CHLOROPHYLL A

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

ChemComp-CL0:
CHLOROPHYLL A ISOMER

ChemComp-PQN:
PHYLLOQUINONE

ChemComp-CHL:
CHLOROPHYLL B

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

Source
  • spinacia oleracea (spinach)
KeywordsELECTRON TRANSPORT / NDH / PSI / Supercomplex / photosynthesis / electron transport chain / lipids / proton translocation / plastoquinone

+
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