8IC3

Respiratory complex Peripheral Arm of CI, focus-refined map 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 1.3 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
Membrane Entity: Yes 
UniProt
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
Membrane Entity: Yes 
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Find proteins for Q9DC70 (Mus musculus)
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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
Membrane Entity: Yes 
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IMPC:  MGI:1915599
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UniProt GroupQ9DCT2
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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
Membrane Entity: Yes 
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Find proteins for Q91WD5 (Mus musculus)
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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
Membrane Entity: Yes 
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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
Membrane Entity: Yes 
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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
Membrane Entity: Yes 
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Find proteins for Q91VD9 (Mus musculus)
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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
Membrane Entity: Yes 
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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
Membrane Entity: Yes 
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Find proteins for Q8K3J1 (Mus musculus)
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IMPC:  MGI:2385079
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialJ [auth P]377Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9DC69 (Mus musculus)
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IMPC:  MGI:1913358
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialK [auth Q]175Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CXZ1 (Mus musculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialL [auth R]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P52503 (Mus musculus)
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IMPC:  MGI:107932
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2M [auth S]99Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQ75 (Mus musculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialN [auth T]156Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CR21 (Mus musculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5O [auth V]116Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CPP6 (Mus musculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6P [auth W]131Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9CQZ5 (Mus musculus)
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IMPC:  MGI:1914380
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UniProt GroupQ9CQZ5
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8Q [auth X]172Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9DCJ5 (Mus musculus)
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IMPC:  MGI:1915625
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UniProt GroupQ9DCJ5
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13R [auth Z]144Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9ERS2 (Mus musculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1S [auth a]70Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for O35683 (Mus musculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3T [auth b]84Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9CQ91 (Mus musculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12U [auth q]145Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7TMF3 (Mus musculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7V [auth r]113Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1913666
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialW [auth s]104Mus musculusMutation(s): 0 
Membrane Entity: Yes 
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IMPC:  MGI:1890894
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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PA [auth q]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ9 (Subject of Investigation/LOI)
Query on UQ9

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

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JA [auth I],
Z [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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HA [auth H],
IA [auth H]
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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MA [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
EHZ (Subject of Investigation/LOI)
Query on EHZ

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OA [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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BA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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CA [auth F]
DA [auth G]
EA [auth G]
KA [auth I]
LA [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ1 (Subject of Investigation/LOI)
Query on UQ1

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

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

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NA [auth R]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: 2024-10-23
    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