8XNM | pdb_00008xnm

Respiratory complex Peripheral Arm of CI, close form B, focus-refined map of type I, Wild type mouse under thermoneutral temperature

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

  • Deposited: 2023-12-30 Released: 2024-10-30 
  • 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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8XNM

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 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: 577.9 kDa 
  • Atom Count: 34,662 
  • Modeled Residue Count: 4,282 
  • Deposited Residue Count: 5,036 
  • Unique protein chains: 23

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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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DC70 (Mus musculus)
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IMPC:  MGI:1922656
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UniProt GroupQ9DC70
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DCT2 (Mus musculus)
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IMPC:  MGI:1915599
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q91WD5 (Mus musculus)
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IMPC:  MGI:2385112
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Reference Sequence
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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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Find proteins for Q9D6J6 (Mus musculus)
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IMPC:  MGI:1920150
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UniProt GroupQ9D6J6
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YT0 (Mus musculus)
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IMPC:  MGI:107851
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q91VD9 (Mus musculus)
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IMPC:  MGI:2443241
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Reference Sequence
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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 
UniProt
Find proteins for P03888 (Mus musculus)
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K3J1 (Mus musculus)
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IMPC:  MGI:2385079
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UniProt GroupQ8K3J1
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DC69 (Mus musculus)
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IMPC:  MGI:1913358
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Reference Sequence
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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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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for P52503 (Mus musculus)
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IMPC:  MGI:107932
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQZ5 (Mus musculus)
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IMPC:  MGI:1914380
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UniProt GroupQ9CQZ5
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DCJ5 (Mus musculus)
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IMPC:  MGI:1915625
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UniProt GroupQ9DCJ5
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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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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UniProt GroupQ9CQ91
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Reference Sequence
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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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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z1P6 (Mus musculus)
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IMPC:  MGI:1913666
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BK30 (Mus musculus)
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IMPC:  MGI:1890894
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
(Subject of Investigation/LOI)

Query on CDL



Download:Ideal Coordinates CCD File
OA [auth q]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
UQ9
(Subject of Investigation/LOI)

Query on UQ9



Download:Ideal Coordinates CCD File
Z [auth D]Ubiquinone-9
C54 H82 O4
UUGXJSBPSRROMU-YJKFELPISA-N
PC1
(Subject of Investigation/LOI)

Query on PC1



Download:Ideal Coordinates CCD File
GA [auth H],
HA [auth I],
PA [auth q]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
(Subject of Investigation/LOI)

Query on 3PE



Download:Ideal Coordinates CCD File
NA [auth b],
X [auth A]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP
(Subject of Investigation/LOI)

Query on NDP



Download:Ideal Coordinates CCD File
KA [auth P]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
EHZ
(Subject of Investigation/LOI)

Query on EHZ



Download:Ideal Coordinates CCD File
MA [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



Download:Ideal Coordinates CCD File
BA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth G]
EA [auth G]
IA [auth I]
JA [auth I]
CA [auth F],
DA [auth G],
EA [auth G],
IA [auth I],
JA [auth I],
Y [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
AA [auth E],
FA [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
LA [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection
  • Version 1.2: 2024-12-04
    Changes: Data collection, Database references