8UGD

In-situ complex III, state I

  • 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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 631: 232-239

  • 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA [auth 3A],
K [auth 3N]
480Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0PK14 (Sus scrofa)
Explore A0A8D0PK14 
Go to UniProtKB:  A0A8D0PK14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D0PK14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB [auth 3B],
L [auth 3O]
453Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RPD2 (Sus scrofa)
Explore F1RPD2 
Go to UniProtKB:  F1RPD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RPD2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth 3C],
M [auth 3P]
379Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q1HBG9 (Sus scrofa)
Explore Q1HBG9 
Go to UniProtKB:  Q1HBG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1HBG9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1D [auth 3D],
N [auth 3Q]
326Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AZF9 (Sus scrofa)
Explore A0A287AZF9 
Go to UniProtKB:  A0A287AZF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AZF9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth 3E],
I [auth 3I],
O [auth 3R],
S [auth 3V]
274Sus scrofaMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for A0A480EHC1 (Sus scrofa)
Explore A0A480EHC1 
Go to UniProtKB:  A0A480EHC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A480EHC1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F [auth 3F],
P [auth 3S]
111Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZPR8 (Sus scrofa)
Explore A0A286ZPR8 
Go to UniProtKB:  A0A286ZPR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286ZPR8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G [auth 3G],
Q [auth 3T]
82Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0SHY6 (Sus scrofa)
Explore A0A8D0SHY6 
Go to UniProtKB:  A0A8D0SHY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D0SHY6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH [auth 3H],
R [auth 3U]
91Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1JI21 (Sus scrofa)
Explore A0A8D1JI21 
Go to UniProtKB:  A0A8D1JI21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1JI21
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 7.2 kDa proteinJ [auth 3J],
T [auth 3W]
64Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1J3N6 (Sus scrofa)
Explore A0A8D1J3N6 
Go to UniProtKB:  A0A8D1J3N6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1J3N6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10U [auth 3X],
V [auth 3Y]
56Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SDI2 (Sus scrofa)
Explore F1SDI2 
Go to UniProtKB:  F1SDI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1SDI2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
DA [auth 3C]
HA [auth 3D]
SA [auth 3P]
TA [auth 3P]
VA [auth 3Q]
DA [auth 3C],
HA [auth 3D],
SA [auth 3P],
TA [auth 3P],
VA [auth 3Q],
W [auth 3A]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10
Query on U10

Download Ideal Coordinates CCD File 
BA [auth 3C],
CA [auth 3C],
PA [auth 3P],
QA [auth 3P]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1
Query on PC1

Download Ideal Coordinates CCD File 
AB [auth 3X],
JA [auth 3E],
YA [auth 3R]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
BB [auth 3Y]
EA [auth 3C]
GA [auth 3D]
KA [auth 3G]
LA [auth 3N]
BB [auth 3Y],
EA [auth 3C],
GA [auth 3D],
KA [auth 3G],
LA [auth 3N],
MA [auth 3N],
RA [auth 3P],
WA [auth 3Q],
X [auth 3A],
Y [auth 3A],
ZA [auth 3R]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
FA [auth 3D],
UA [auth 3Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth 3C],
NA [auth 3P],
OA [auth 3P],
Z [auth 3C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES
Query on FES

Download Ideal Coordinates CCD File 
IA [auth 3E],
XA [auth 3R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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
  • Version 1.1: 2024-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary