8IB9

Respiratory complex CI:CIII2, 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: 4.30 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
NADH-ubiquinone oxidoreductase chain 3115Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03899 (Mus musculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial224Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1922656
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial263Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1915599
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial463Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2385112
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial248Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:1920150
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial464Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:107851
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial727Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2443241
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1318Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial212Mus musculusMutation(s): 0 
EC: 7.1.1.2
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IMPC:  MGI:2385079
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6172Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Find proteins for P03925 (Mus musculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4L98Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5607Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4459Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2345Mus musculusMutation(s): 0 
EC: 7.1.1.2
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial355Mus musculusMutation(s): 0 
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IMPC:  MGI:1914523
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial377Mus musculusMutation(s): 0 
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IMPC:  MGI:1913358
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial175Mus musculusMutation(s): 0 
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Find proteins for Q9CXZ1 (Mus musculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial116Mus musculusMutation(s): 0 
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IMPC:  MGI:107932
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 299Mus musculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrial
T, U
156Mus musculusMutation(s): 0 
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Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5116Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6131Mus musculusMutation(s): 0 
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IMPC:  MGI:1914380
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8172Mus musculusMutation(s): 0 
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IMPC:  MGI:1915625
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11143Mus musculusMutation(s): 0 
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IMPC:  MGI:1917125
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13144Mus musculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1AA [auth a]70Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3BA [auth b]84Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialCA [auth c]76Mus musculusMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2DA [auth d]120Mus musculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5EA [auth e]106Mus musculusMutation(s): 0 
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IMPC:  MGI:1890889
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1FA [auth f]57Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialGA [auth g]151Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialHA [auth h]189Mus musculusMutation(s): 0 
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IMPC:  MGI:1913296
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6IA [auth i]128Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialJA [auth j]105Mus musculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3KA [auth k]104Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialLA [auth l]186Mus musculusMutation(s): 0 
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IMPC:  MGI:1914514
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4MA [auth m]129Mus musculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9NA [auth n]179Mus musculusMutation(s): 0 
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IMPC:  MGI:1913468
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7OA [auth o]137Mus musculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10PA [auth p]176Mus musculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12QA [auth q]145Mus musculusMutation(s): 0 
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Find proteins for Q7TMF3 (Mus musculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7RA [auth r]113Mus musculusMutation(s): 0 
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IMPC:  MGI:1913666
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialSA [auth s]104Mus musculusMutation(s): 0 
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IMPC:  MGI:1890894
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialEB [auth Aa],
TA [auth AA]
480Mus musculusMutation(s): 0 
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IMPC:  MGI:107876
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialFB [auth Ab],
UA [auth AB]
453Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9DB77 (Mus musculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bGB [auth Ac],
VA [auth AC]
381Mus musculusMutation(s): 0 
UniProt
Find proteins for P00158 (Mus musculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialHB [auth Ad],
WA [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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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialBB [auth AI],
IB [auth Ae],
XA [auth AE]
274Mus musculusMutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for Q9CR68 (Mus musculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7JB [auth Af],
YA [auth AF]
111Mus musculusMutation(s): 0 
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Find proteins for Q9CQB4 (Mus musculus)
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IMPC:  MGI:1914780
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8KB [auth Ag],
ZA [auth AG]
82Mus musculusMutation(s): 0 
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Find proteins for Q9CQ69 (Mus musculus)
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IMPC:  MGI:107807
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAB [auth AH],
LB [auth Ah]
89Mus musculusMutation(s): 0 
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Find proteins for P99028 (Mus musculus)
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IMPC:  MGI:1913826
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9CB [auth AJ],
MB [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: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10DB [auth AK],
NB [auth Ak]
56Mus musculusMutation(s): 0 
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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IC [auth L]
ID [auth Aa]
JC [auth L]
OD [auth Ac]
QD [auth Ag]
IC [auth L],
ID [auth Aa],
JC [auth L],
OD [auth Ac],
QD [auth Ag],
TC [auth a],
VC [auth d],
WC [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10 (Subject of Investigation/LOI)
Query on U10

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FD [auth AC],
MD [auth Ac]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
UQ9 (Subject of Investigation/LOI)
Query on UQ9

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YB [auth H]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC1 (Subject of Investigation/LOI)
Query on PC1

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AC [auth I],
KC [auth L],
QB [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE (Subject of Investigation/LOI)
Query on 3PE

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AD [auth m]
DC [auth J]
EC [auth K]
ED [auth AC]
FC [auth L]
AD [auth m],
DC [auth J],
EC [auth K],
ED [auth AC],
FC [auth L],
GC [auth L],
HC [auth L],
LC [auth M],
LD [auth Ac],
MC [auth M],
NC [auth M],
OC [auth O],
RB [auth D],
UC [auth b],
XC [auth i],
YC [auth j],
ZB [auth I],
ZC [auth m]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP (Subject of Investigation/LOI)
Query on NDP

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QC [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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

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CD [auth AC],
DD [auth AC],
JD [auth Ac],
KD [auth Ac]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ6 (Subject of Investigation/LOI)
Query on UQ6

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GD [auth AC],
ND [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
EHZ (Subject of Investigation/LOI)
Query on EHZ

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BD [auth n],
SC [auth W]
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
C25 H49 N2 O9 P S
JYSKQPQRUCZFIQ-REWPJTCUSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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TB [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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PC [auth O]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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BC [auth I]
CC [auth I]
OB [auth B]
UB [auth F]
VB [auth G]
BC [auth I],
CC [auth I],
OB [auth B],
UB [auth F],
VB [auth G],
WB [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ1 (Subject of Investigation/LOI)
Query on UQ1

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PB [auth B]UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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SB [auth E],
XB [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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RC [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2024-12-04
    Changes: Data collection, Database references