[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 respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Journal, issue, pagesNat Plants, Vol. 9, Issue 1, Page 142-156, Year 2023
Publish dateDec 30, 2022
AuthorsNiklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
PubMed AbstractProtein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
External linksNat Plants / PubMed:36585502 / PubMed Central
MethodsEM (single particle)
Resolution2.03 - 2.8 Å
Structure data

EMDB-15998, PDB-8bed:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral tip)
Method: EM (single particle) / Resolution: 2.03 Å

EMDB-15999, PDB-8bee:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)
Method: EM (single particle) / Resolution: 2.04 Å

EMDB-16000, PDB-8bef:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
Method: EM (single particle) / Resolution: 2.13 Å

EMDB-16003, PDB-8beh:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-16007, PDB-8bel:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII membrane domain)
Method: EM (single particle) / Resolution: 2.25 Å

EMDB-16008, PDB-8bep:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CIII MPP domain)
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-16153: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
Method: EM (single particle) / Resolution: 2.09 Å

EMDB-16156: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 1 membrane arm)
Method: EM (single particle) / Resolution: 2.53 Å

EMDB-16166: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 2 consensus)
Method: EM (single particle) / Resolution: 2.79 Å

EMDB-16167: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 1 consensus)
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-16168, PDB-8bpx:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete composition)
Method: EM (single particle) / Resolution: 2.09 Å

EMDB-16171, PDB-8bq5:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 1 composition)
Method: EM (single particle) / Resolution: 2.73 Å

EMDB-16172, PDB-8bq6:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete conformation 2 composition)
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

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

ChemComp-UQ9:
Ubiquinone-9

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

ChemComp-FE:
Unknown entry

ChemComp-UQ5:
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE

ChemComp-PC7:
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-BCO:
Butyryl Coenzyme A

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-UQ7:
UBIQUINONE-7

ChemComp-COO:
CROTONYL COENZYME A

Source
  • arabidopsis thaliana (thale cress)
  • Arabidopsis t (thale cress)
  • thale cress (thale cress)
KeywordsMEMBRANE PROTEIN / Plant / Mitochondria / Comple. / 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