8IBC

Respiratory complex CIII2, focus-refined of type IB, Wild type mouse under cold temperature

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2023-02-10 Released: 2024-09-18 
  • Deposition Author(s): Shin, Y.-C., Liao, M.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of respiratory complex adaptation to cold temperatures.

Shin, Y.C.Latorre-Muro, P.Djurabekova, A.Zdorevskyi, O.Bennett, C.F.Burger, N.Song, K.Xu, C.Paulo, J.A.Gygi, S.P.Sharma, V.Liao, M.Puigserver, P.

(2024) Cell 187: 6584

  • DOI: https://doi.org/10.1016/j.cell.2024.09.029
  • Primary Citation of Related Structures:  
    8IAO, 8IAP, 8IAQ, 8IAR, 8IB4, 8IB5, 8IB6, 8IB7, 8IB9, 8IBA, 8IBB, 8IBC, 8IBD, 8IBE, 8IBF, 8IBG, 8IC2, 8IC3, 8IC4, 8IC5, 8XNL, 8XNM, 8XNN, 8XNO, 8XNP, 8XNQ, 8XNR, 8XNS, 8XNT, 8XNU, 8XNV, 8XNW, 8XNX, 8XNY, 8XNZ, 8XO0

  • PubMed Abstract: 

    In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation upon cold exposure remains elusive. Herein, we combined thermoregulatory physiology and cryoelectron microscopy (cryo-EM) to study endogenous respiratory supercomplexes from mice exposed to different temperatures. A cold-induced conformation of CI:III 2 (termed type 2) supercomplex was identified with a ∼25° rotation of CIII 2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting catalytic states that favor electron transfer. Large-scale supercomplex simulations in mitochondrial membranes reveal how lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations, and biochemical analyses unveil the thermoregulatory mechanisms and dynamics of increased respiratory capacity in brown fat at the structural and energetic level.


  • Organizational Affiliation

    Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA [auth AA],
L [auth Aa]
480Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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IMPC:  MGI:107876
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UniProt GroupQ9CZ13
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB [auth AB],
M [auth Ab]
453Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9DB77 (Mus musculus)
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UniProt GroupQ9DB77
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth AC],
N [auth Ac]
381Mus musculusMutation(s): 0 
UniProt
Find proteins for P00158 (Mus musculus)
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UniProt GroupP00158
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD [auth AD],
O [auth Ad]
325Mus musculusMutation(s): 0 
EC: 7.1.1.8
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Find proteins for Q9D0M3 (Mus musculus)
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IMPC:  MGI:1913695
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UniProt GroupQ9D0M3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth AE],
I [auth AI],
P [auth Ae]
274Mus musculusMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for Q9CR68 (Mus musculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F [auth AF],
Q [auth Af]
111Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQB4 (Mus musculus)
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IMPC:  MGI:1914780
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UniProt GroupQ9CQB4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G [auth AG],
R [auth Ag]
82Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQ69 (Mus musculus)
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IMPC:  MGI:107807
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UniProt GroupQ9CQ69
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH [auth AH],
S [auth Ah]
89Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P99028 (Mus musculus)
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IMPC:  MGI:1913826
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UniProt GroupP99028
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J [auth AJ],
T [auth Aj]
64Mus musculusMutation(s): 0 
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Find proteins for Q8R1I1 (Mus musculus)
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IMPC:  MGI:1913402
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10K [auth AK],
U [auth Ak]
56Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CPX8 (Mus musculus)
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BA [auth Aa],
HA [auth Ac],
JA [auth Ag]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10 (Subject of Investigation/LOI)
Query on U10

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FA [auth Ac],
Y [auth AC]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
3PE (Subject of Investigation/LOI)
Query on 3PE

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EA [auth Ac],
X [auth AC]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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AA [auth AD],
IA [auth Ad]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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CA [auth Ac],
DA [auth Ac],
V [auth AC],
W [auth AC]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ6 (Subject of Investigation/LOI)
Query on UQ6

Download Ideal Coordinates CCD File 
GA [auth Ac],
Z [auth AC]
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRO1 DK081418
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRO1 DK089883

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-06
    Changes: Data collection
  • Version 1.3: 2024-12-04
    Changes: Data collection, Database references