Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang /
PubMed Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
EMDB-42143, PDB-8ud1: High resolution in-situ structure of complex I in respiratory supercomplex (composite) Method: EM (single particle) / Resolution: 2.1 Å
EMDB-42225, PDB-8ugh: In-situ structure of typeA supercomplex with lipids in respiratory chain (composite) Method: EM (single particle) / Resolution: 2.1 Å
EMDB-42226, PDB-8ugi: High resolution in-situ structure of typeA supercomplex in respiratory chain (I1III2IV1,composite) Method: EM (single particle) / Resolution: 2.1 Å
EMDB-42228, PDB-8ugk: High resolution in-situ structure of complex III in respiratory supercomplex (composite) Method: EM (single particle) / Resolution: 2.1 Å
EMDB-42231, PDB-8ugp: In-situ structure of typeA supercomplex in respiratory chain ( local refined map focused on CI iron-sulfur cluster regions ) Method: EM (single particle) / Resolution: 2.0 Å
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
Movie
Controller
Structure viewers
About Yorodumi Papers
Authors
External links
Keywords
ELECTRON TRANSPORT / in-situ cryo-EM structure / 
