[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

TitleStructures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Journal, issue, pagesMol Cell, Vol. 75, Issue 6, Page 1131-11146.e6, Year 2019
Publish dateSep 19, 2019
AuthorsJames A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
PubMed AbstractThe mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
External linksMol Cell / PubMed:31492636 / PubMed Central
MethodsEM (single particle)
Resolution3.8 - 7.5 Å
Structure data

EMDB-4479, PDB-6q9b:
CI Membrane Arm focused refinement from Ovine respiratory SC I+III2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-4480, PDB-6q9d:
CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-4481, PDB-6q9e:
Complex III2 focused refinement from Ovine respiratory supercomplex I+III2
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-4482, PDB-6qa9:
Isolated complex I class refinement from Ovine respiratory supercomplex I+III2
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-4493, PDB-6qbx:
Ovine respiratory supercomplex I+III2 closed class.
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-4494, PDB-6qc2:
Ovine respiratory supercomplex I+III2 open class 2
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-4495, PDB-6qc3:
Ovine respiratory supercomplex I+III2 open class 1
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-4496, PDB-6qc4:
Ovine respiratory supercomplex I+III2 open class 3
Method: EM (single particle) / Resolution: 4.6 Å

EMDB-4497, PDB-6qc5:
Ovine respiratory complex I FRC closed class 1
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-4498, PDB-6qc6:
Ovine respiratory complex I FRC open class 1
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-4499, PDB-6qc7:
Ovine respiratory complex I FRC open class 3
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-4500, PDB-6qc8:
Ovine respiratory complex I FRC open class 2
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-4501, PDB-6qc9:
Ovine respiratory complex I FRC open class 4
Method: EM (single particle) / Resolution: 5.7 Å

EMDB-4502, PDB-6qca:
Ovine respiratory complex I FRC open class 5
Method: EM (single particle) / Resolution: 6.2 Å

EMDB-4505, PDB-6qcf:
Ovine respiratory complex I FRC open class 6
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-4506:
Ovine respiratory complex I FRC poor closed class
Method: EM (single particle) / Resolution: 7 Å

EMDB-4507:
Ovine respiratory complex I FRC poor open class
Method: EM (single particle) / Resolution: 7.5 Å

Chemicals

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

ChemComp-ZMP:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

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

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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

ChemComp-ZN:
Unknown entry

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

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

ChemComp-HEC:
HEME C / Heme C

Source
  • ovis aries (sheep)
  • Sheep (sheep)
KeywordsELECTRON TRANSPORT / complex I / membrane arm / cellular respiration / mitochondria / peripheral arm / complex III / supercomplex

+
About Yorodumi Papers

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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