8IBC | pdb_00008ibc

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

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Mus musculus
  • Mutation(s): No 
  • Membrane Protein: Yes  mpstruc

  • 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

Validation slider image for 8IBC

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 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.

Macromolecule Content 

  • Total Structure Weight: 556.01 kDa 
  • Atom Count: 31,431 
  • Modeled Residue Count: 3,915 
  • Deposited Residue Count: 4,904 
  • Unique protein chains: 10

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 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CZ13 (Mus musculus)
Explore Q9CZ13 
Go to UniProtKB:  Q9CZ13
IMPC:  MGI:107876
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UniProt GroupQ9CZ13
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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt
Find proteins for Q9DB77 (Mus musculus)
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UniProt GroupQ9DB77
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome bC [auth AC],
N [auth Ac]
381Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00158 (Mus musculus)
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UniProt GroupP00158
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Reference Sequence
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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
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D0M3 (Mus musculus)
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IMPC:  MGI:1913695
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UniProt GroupQ9D0M3
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Reference Sequence
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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
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR68 (Mus musculus)
Explore Q9CR68 
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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQB4 (Mus musculus)
Explore Q9CQB4 
Go to UniProtKB:  Q9CQB4
IMPC:  MGI:1914780
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UniProt GroupQ9CQB4
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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQ69 (Mus musculus)
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Go to UniProtKB:  Q9CQ69
IMPC:  MGI:107807
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UniProt GroupQ9CQ69
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Reference Sequence
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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 
Membrane Entity: Yes 
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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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R1I1 (Mus musculus)
Explore Q8R1I1 
Go to UniProtKB:  Q8R1I1
IMPC:  MGI:1913402
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Reference Sequence
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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 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPX8 (Mus musculus)
Explore Q9CPX8 
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
(Subject of Investigation/LOI)

Query on CDL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
FA [auth Ac],
Y [auth AC]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
3PE
(Subject of Investigation/LOI)

Query on 3PE



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
AA [auth AD],
IA [auth Ad]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
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