8IC4

Respiratory complex Membrane domain of CI, focus-refined of type I, PERK -/- mouse under cold temperature

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

  • 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: 3.20 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

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 

  • 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 dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialA [auth D]463Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
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IMPC:  MGI:2385112
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UniProt GroupQ91WD5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6B [auth J]172Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03925 (Mus musculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LC [auth K]98Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
Find proteins for P03903 (Mus musculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5D [auth L]607Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4E [auth M]459Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2F [auth N]345Mus musculusMutation(s): 0 
EC: 7.1.1.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialG [auth O]355Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q99LC3 (Mus musculus)
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IMPC:  MGI:1914523
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialH [auth U]156Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8I [auth X]172Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1915625
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11J [auth Y]143Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1917125
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialK [auth c]76Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQY9 (Mus musculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2L [auth d]120Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5M [auth e]106Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q99LY9 (Mus musculus)
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IMPC:  MGI:1890889
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1N [auth f]57Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialO [auth g]151Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialP [auth h]189Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913296
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6Q [auth i]128Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q3UIU2 (Mus musculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialR [auth j]105Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPU2 (Mus musculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3S [auth k]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQZ6 (Mus musculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialT [auth l]186Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1914514
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UniProt GroupQ9D6J5
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4U [auth m]129Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQC7 (Mus musculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9V [auth n]179Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913468
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7W [auth o]137Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR61 (Mus musculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10X [auth p]176Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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CA [auth L],
HA [auth M],
JA [auth Y],
KA [auth d],
LA [auth h]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
3PE (Subject of Investigation/LOI)
Query on 3PE

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AA [auth L]
BA [auth L]
EA [auth L]
FA [auth M]
GA [auth M]
AA [auth L],
BA [auth L],
EA [auth L],
FA [auth M],
GA [auth M],
MA [auth i],
NA [auth m],
Y [auth D],
Z [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
EHZ (Subject of Investigation/LOI)
Query on EHZ

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OA [auth n]~{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
ADP (Subject of Investigation/LOI)
Query on ADP

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

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DA [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2024-11-13
    Changes: Data collection