8UGP

In-situ structure of typeA supercomplex in respiratory chain ( local refined map focused on CI iron-sulfur cluster regions )

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2023-10-05 Released: 2024-06-19 
  • Deposition Author(s): Zheng, W., Zhang, K., Zhu, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

High-resolution in situ structures of mammalian respiratory supercomplexes.

Zheng, W.Chai, P.Zhu, J.Zhang, K.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07488-9
  • Primary Citation of Related Structures:  
    8UD1, 8UEO, 8UEP, 8UEQ, 8UER, 8UES, 8UET, 8UEU, 8UEV, 8UEW, 8UEX, 8UEY, 8UEZ, 8UGD, 8UGE, 8UGF, 8UGG, 8UGH, 8UGI, 8UGJ, 8UGK, 8UGL, 8UGN, 8UGP, 8UGR

  • 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 1-4 . 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: I 1 III 2 IV 1 , I 1 III 2 IV 2 , I 2 III 2 IV 2 and I 2 III 4 IV 2 , 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.


  • Organizational Affiliation

    School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A [auth 1A]115Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupO79880
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialB [auth 1B]258Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VVS8 (Sus scrofa)
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UniProt GroupA0A4X1VVS8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialC [auth 1C]264Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNN4 (Sus scrofa)
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UniProt GroupA0A286ZNN4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialD [auth 1D]476Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0QM68 (Sus scrofa)
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UniProt GroupA0A8D0QM68
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialE [auth 1G]727Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1AAL8 (Sus scrofa)
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UniProt GroupA0A8D1AAL8
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1F [auth 1H]318Sus scrofaMutation(s): 0 
EC: 7.1.1.2
UniProt
Find proteins for A0A0U1RS44 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialG [auth 1I]239Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZUN9 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialH [auth 1P]377Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1ULW2 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialI [auth 1Q]175Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SN37 (Sus scrofa)
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UniProt GroupA0A4X1SN37
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialJ [auth 1R]123Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1THU2 (Sus scrofa)
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UniProt GroupA0A4X1THU2
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6K [auth 1W]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480VKQ8 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12L [auth 1q]145Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SJF2 (Sus scrofa)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM142959

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release