8UGL

High resolution in-situ structure of complex IV in respiratory supercomplex

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

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
Cytochrome c oxidase subunit 1A [auth 4A]514Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B [auth 4B]229Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q69GF7 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C [auth 4C]261Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4D [auth 4D]169Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1T8J9 (Sus scrofa)
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UniProt GroupA0A4X1T8J9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialE [auth 4E]152Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrialF [auth 4F]129Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2G [auth 4G]97Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H [auth 4H]86Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI [auth 4I]75Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrialJ [auth 4J]80Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7BK [auth 4K]80Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialL [auth 4L]63Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8M [auth 4M]70Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA1XQT4
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit NDUFA4N [auth 4N]82Sus scrofaMutation(s): 0 
UniProt
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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FA [auth 4C],
HA [auth 4D],
X [auth 4B]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA (Subject of Investigation/LOI)
Query on HEA

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R [auth 4A],
S [auth 4A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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KA [auth 4G],
LA [auth 4G]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
PSC
Query on PSC

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Z [auth 4B](7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
PGV
Query on PGV

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AA [auth 4C]
BA [auth 4C]
CA [auth 4C]
DA [auth 4C]
EA [auth 4C]
AA [auth 4C],
BA [auth 4C],
CA [auth 4C],
DA [auth 4C],
EA [auth 4C],
GA [auth 4C],
JA [auth 4G],
NA [auth 4J],
O [auth 4A],
OA [auth 4K],
P [auth 4A],
PA [auth 4L],
Q [auth 4A],
QA [auth 4M],
W [auth 4B]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
CUA
Query on CUA

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Y [auth 4B]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

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MA [auth 4H]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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IA [auth 4F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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T [auth 4A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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U [auth 4A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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V [auth 4A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B [auth 4B]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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