[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

TitleA ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Journal, issue, pagesPlant Cell, Vol. 33, Issue 6, Page 2072-2091, Year 2021
Publish dateJul 19, 2021
AuthorsNiklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
PubMed AbstractMitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
External linksPlant Cell / PubMed:33768254 / PubMed Central
MethodsEM (single particle)
Resolution2.88 - 3.72 Å
Structure data

11872

7aqq

EMDB-11872, PDB-7aqq:
Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core)
Method: EM (single particle) / Resolution: 3.06 Å

11873

7aqr

EMDB-11873, PDB-7aqr:
Cryo-EM structure of Arabidopsis thaliana Complex-I (peripheral arm)
Method: EM (single particle) / Resolution: 2.91 Å

11874

7aqw

EMDB-11874, PDB-7aqw:
Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip)
Method: EM (single particle) / Resolution: 3.17 Å

11875

7ar7

EMDB-11875, PDB-7ar7:
Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
Method: EM (single particle) / Resolution: 3.72 Å

11876

7ar8

EMDB-11876, PDB-7ar8:
Cryo-EM structure of Arabidopsis thaliana complex-I (closed conformation)
Method: EM (single particle) / Resolution: 3.53 Å

11877

7ar9

EMDB-11877, PDB-7ar9:
Cryo-EM structure of Polytomella Complex-I (membrane arm)
Method: EM (single particle) / Resolution: 2.97 Å

11878

7arb

EMDB-11878, PDB-7arb:
Cryo-EM structure of Arabidopsis thaliana Complex-I (complete composition)
Method: EM (single particle) / Resolution: 3.41 Å

11879

7arc

EMDB-11879, PDB-7arc:
Cryo-EM structure of Polytomella Complex-I (peripheral arm)
Method: EM (single particle) / Resolution: 2.88 Å

11880

7ard

EMDB-11880, PDB-7ard:
Cryo-EM structure of Polytomella Complex-I (complete composition)
Method: EM (single particle) / Resolution: 3.11 Å

Chemicals

ChemComp-UQ9:
Ubiquinone-9

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

ChemComp-LMN:
Lauryl Maltose Neopentyl Glycol / detergent*YM

ChemComp-FE:
Unknown entry / Iron

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 / Phosphatidylcholine

ChemComp-ZN:
Unknown entry

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

ChemComp-PSF:
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Phosphatidylserine

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

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

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

ChemComp-HOH:
WATER / Water

Source
  • arabidopsis thaliana (thale cress)
  • Mouse-ear cress (thale cress)
  • thale cress (thale cress)
  • polytomella sp. pringsheim 198.80 (plant)
KeywordsELECTRON TRANSPORT / Complex-I / Complex-I Arabidopsis

+
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