8UGD | pdb_00008ugd

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

Validation slider image for 8UGD

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 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.

Macromolecule Content 

  • Total Structure Weight: 599.62 kDa 
  • Atom Count: 33,543 
  • Modeled Residue Count: 4,113 
  • Deposited Residue Count: 5,180 
  • Unique protein chains: 10

Macromolecules

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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)
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UniProt GroupA0A8D0PK14
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Reference Sequence
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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)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bC [auth 3C],
M [auth 3P]
379Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q1HBG9 (Sus scrofa)
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UniProt GroupQ1HBG9
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1D [auth 3D],
N [auth 3Q]
326Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AZF9 (Sus scrofa)
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UniProt GroupA0A287AZF9
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Reference Sequence
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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 A0A4X1TWD8 (Sus scrofa)
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UniProt GroupA0A4X1TWD8
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Reference Sequence
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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)
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Reference Sequence
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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)
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UniProt GroupA0A8D0SHY6
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Reference Sequence
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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)
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Reference Sequence
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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 Q2EN79 (Sus scrofa)
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Reference Sequence
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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)
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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

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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
  • Version 1.1: 2024-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary