[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleCryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 6903, Year 2021
Publish dateNov 25, 2021
AuthorsF Kolbe / S Safarian / Ż Piórek / S Welsch / H Müller / H Michel /
PubMed AbstractCytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) ...Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.
External linksNat Commun / PubMed:34824221 / PubMed Central
MethodsEM (single particle)
Resolution2.4 - 2.66 Å
Structure data

EMDB-11921, PDB-7ate:
Cytochrome c oxidase structure in P-state
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-11922, PDB-7atn:
Cytochrome c oxidase structure in R-state
Method: EM (single particle) / Resolution: 2.66 Å

EMDB-11924, PDB-7au3:
Cytochrome c oxidase structure in F-state
Method: EM (single particle) / Resolution: 2.56 Å

EMDB-11925, PDB-7au6:
Cytochrome c oxidase structure in O-state
Method: EM (single particle) / Resolution: 2.4 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-HEA:
HEME-A

ChemComp-CU:
COPPER (II) ION

ChemComp-CA:
Unknown entry

ChemComp-PEO:
HYDROGEN PEROXIDE

ChemComp-CUA:
DINUCLEAR COPPER ION

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

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

ChemComp-HOH:
WATER

ChemComp-O:
OXYGEN ATOM

ChemComp-2FK:
SUPEROXO ION

ChemComp-OXY:
OXYGEN MOLECULE

Source
  • paracoccus denitrificans (bacteria)
KeywordsMEMBRANE PROTEIN / Terminal oxidase Cytochrome c oxidase aa3 oxidase

+
About EMN 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

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.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

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more