8UCA

Formation of I2+III2 supercomplex rescues respiratory chain defects

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Formation of I 2 +III 2 supercomplex rescues respiratory chain defects.

Liang, C., Padavannil, A., Zhang, S., Beh, S., Robinson, D.R.L., Meisterknecht, J., Cabrera-Orefice, A., Koves, T.R., Watanabe, C., Watanabe, M., Illescas, M., Lim, R., Johnson, J.M., Ren, S., Wu, Y.J., Kappei, D., Ghelli, A.M., Funai, K., Osaka, H., Muoio, D., Ugalde, C., Wittig, I., Stroud, D.A., Letts, J.A., Ho, L.

(2025) Cell Metab 37: 441-459.e11

  • DOI: https://doi.org/10.1016/j.cmet.2024.11.011
  • Primary Citation of Related Structures:  
    8UCA

  • PubMed Abstract: 

    Mitochondrial electron transport chain (ETC) complexes partition between free complexes and quaternary assemblies known as supercomplexes (SCs). However, the physiological requirement for SCs and the mechanisms regulating their formation remain controversial. Here, we show that genetic perturbations in mammalian ETC complex III (CIII) biogenesis stimulate the formation of a specialized extra-large SC (SC-XL) with a structure of I 2 +III 2 , resolved at 3.7 Å by cryoelectron microscopy (cryo-EM). SC-XL formation increases mitochondrial cristae density, reduces CIII reactive oxygen species (ROS), and sustains normal respiration despite a 70% reduction in CIII activity, effectively rescuing CIII deficiency. Consequently, inhibiting SC-XL formation in CIII mutants using the Uqcrc1 DEL:E258-D260 contact site mutation leads to respiratory decompensation. Lastly, SC-XL formation promotes fatty acid oxidation (FAO) and protects against ischemic heart failure in mice. Our study uncovers an unexpected plasticity in the mammalian ETC, where structural adaptations mitigate intrinsic perturbations, and suggests that manipulating SC-XL formation is a potential therapeutic strategy for mitochondrial dysfunction.

    • Organizational Affiliation: 

    Cardiovascular and Metabolic Diseases, Duke-NUS Medical School, Singapore, Singapore.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3A [auth 3],
OA [auth 3a]		115Mus musculusMutation(s): 0 
Gene Names: mt-Nd3
EC: 7.1.1.2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialB [auth S3],
PA [auth s3]		263Mus musculusMutation(s): 0 
Gene Names: Ndufs3
EC: 7.1.1.2
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IMPC:  MGI:1915599
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialC [auth S2],
QA [auth s2]		463Mus musculusMutation(s): 0 
Gene Names: Ndufs2
EC: 7.1.1.2
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IMPC:  MGI:2385112
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1D [auth 1],
RA [auth 1a]		318Mus musculusMutation(s): 0 
Gene Names: mt-Nd1, ND1
EC: 7.1.1.2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 6E [auth 6],
SA [auth 6a]		172Mus musculusMutation(s): 0 
Gene Names: Mtnd6, mt-Nd6, Nd6
EC: 7.1.1.2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4LF [auth 4L],
TA [auth 4l]		98Mus musculusMutation(s): 0 
Gene Names: Mtnd4l, mt-Nd4l, Nd4l
EC: 7.1.1.2
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 5G [auth 5],
UA [auth 5a]		607Mus musculusMutation(s): 0 
Gene Names: Mtnd5, mt-Nd5, Nd5
EC: 7.1.1.2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4H [auth 4],
VA [auth 4a]		459Mus musculusMutation(s): 0 
Gene Names: Mtnd4, mt-Nd4, Nd4
EC: 7.1.1.2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 2I [auth 2],
WA [auth 2a]		345Mus musculusMutation(s): 0 
Gene Names: mt-Nd2, Nd2
EC: 7.1.1.2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialJ [auth AL],
XA [auth al]		355Mus musculusMutation(s): 0 
Gene Names: Ndufa10
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IMPC:  MGI:1914523
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialK [auth A9],
YA [auth a9]		377Mus musculusMutation(s): 0 
Gene Names: Ndufa9
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IMPC:  MGI:1913358
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialL [auth S4],
ZA [auth s4]		175Mus musculusMutation(s): 0 
Gene Names: Ndufs4
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrialAB [auth s6],
M [auth S6]		116Mus musculusMutation(s): 0 
Gene Names: Ndufs6, Ip13
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IMPC:  MGI:107932
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2BB [auth a2],
N [auth A2]		99Mus musculusMutation(s): 0 
Gene Names: Ndufa2
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialCB [auth ab],
DB [auth ac],
O [auth AB],
P [auth AC]		156Mus musculusMutation(s): 0 
Gene Names: Ndufab1
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5EB [auth a5],
Q [auth A5]		116Mus musculusMutation(s): 0 
Gene Names: Ndufa5
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6FB [auth a6],
R [auth A6]		131Mus musculusMutation(s): 0 
Gene Names: Ndufa6
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IMPC:  MGI:1914380
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8GB [auth a8],
S [auth A8]		172Mus musculusMutation(s): 0 
Gene Names: Ndufa8
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IMPC:  MGI:1915625
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11HB [auth am],
T [auth AM]		142Mus musculusMutation(s): 0 
Gene Names: Ndufa11
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IMPC:  MGI:1917125
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13IB [auth ao],
U [auth AO]		144Mus musculusMutation(s): 0 
Gene Names: Ndufa13, Grim19
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1JB [auth a1],
V [auth A1]		70Mus musculusMutation(s): 0 
Gene Names: Ndufa1
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3KB [auth a3],
W [auth A3]		84Mus musculusMutation(s): 0 
Gene Names: Ndufa3
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrialLB [auth c1],
X [auth C1]		76Mus musculusMutation(s): 0 
Gene Names: Ndufc1
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 subunit C2MB [auth c2],
Y [auth C2]		120Mus musculusMutation(s): 0 
Gene Names: Ndufc2
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5NB [auth s5],
Z [auth S5]		106Mus musculusMutation(s): 0 
Gene Names: Ndufs5
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IMPC:  MGI:1890889
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1AA [auth B1],
OB [auth b1]		57Mus musculusMutation(s): 0 
Gene Names: Ndufb1
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrialBA [auth BM],
PB [auth bm]		151Mus musculusMutation(s): 0 
Gene Names: Ndufb11, Np15
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrialCA [auth B5],
QB [auth b5]		189Mus musculusMutation(s): 0 
Gene Names: Ndufb5
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IMPC:  MGI:1913296
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6DA [auth B6],
RB [auth b6]		127Mus musculusMutation(s): 0 
Gene Names: Ndufb6, Gm137
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrialEA [auth B2],
SB [auth b2]		105Mus musculusMutation(s): 0 
Gene Names: Ndufb2
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3FA [auth B3],
TB [auth b3]		104Mus musculusMutation(s): 0 
Gene Names: Ndufb3
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrialGA [auth B8],
UB [auth b8]		186Mus musculusMutation(s): 0 
Gene Names: Ndufb8
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IMPC:  MGI:1914514
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4HA [auth B4],
VB [auth b4]		129Mus musculusMutation(s): 0 
Gene Names: Ndufb4
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9IA [auth B9],
WB [auth b9]		179Mus musculusMutation(s): 0 
Gene Names: Ndufb9
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IMPC:  MGI:1913468
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7JA [auth B7],
XB [auth b7]		136Mus musculusMutation(s): 0 
Gene Names: Ndufb7
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10KA [auth BL],
YB [auth bl]		176Mus musculusMutation(s): 0 
Gene Names: Ndufb10
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12LA [auth AN],
ZB [auth an]		145Mus musculusMutation(s): 0 
Gene Names: Ndufa12
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7AC [auth a7],
MA [auth A7]		112Mus musculusMutation(s): 0 
Gene Names: Ndufa7
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IMPC:  MGI:1913666
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrialBC [auth v3],
NA [auth V3]		104Mus musculusMutation(s): 0 
Gene Names: Ndufv3
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IMPC:  MGI:1890894
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialCC [auth 3A],
MC [auth 3L]		446Mus musculusMutation(s): 0 
Gene Names: Uqcrc1
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IMPC:  MGI:107876
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialDC [auth 3B],
NC [auth 3M]		439Mus musculusMutation(s): 0 
Gene Names: Uqcrc2
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bEC [auth 3C],
OC [auth 3N]		380Mus musculusMutation(s): 0 
Gene Names: Mt-Cyb
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialFC [auth 3D],
PC [auth 3O]		241Mus musculusMutation(s): 0 
Gene Names: Cyc1
EC: 7.1.1.8
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IMPC:  MGI:1913695
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9GC [auth 3E],
QC [auth 3P]		196Mus musculusMutation(s): 0 
Gene Names: Uqcrfs1
EC: 7.1.1.8
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7HC [auth 3F],
RC [auth 3Q]		110Mus musculusMutation(s): 0 
Gene Names: Uqcrb
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IMPC:  MGI:1914780
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8IC [auth 3G],
SC [auth 3R]		81Mus musculusMutation(s): 0 
Gene Names: Uqcrq
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IMPC:  MGI:107807
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialJC [auth 3H],
TC [auth 3S]		76Mus musculusMutation(s): 0 
Gene Names: Uqcrh
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IMPC:  MGI:1913826
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9KC [auth 3J],
VC [auth 3U]		63Mus musculusMutation(s): 0 
Gene Names: Uqcr10
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IMPC:  MGI:1913402
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10LC [auth 3K],
WC [auth 3V]		56Mus musculusMutation(s): 0 
Gene Names: Uqcr11, Uqcr
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialUC [auth 3T]78Mus musculusMutation(s): 0 
Gene Names: Uqcrfs1
EC: 7.1.1.8
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialCD [auth v1],
XC [auth V1]		457Mus musculusMutation(s): 0 
Gene Names: Ndufv1
EC: 7.1.1.2
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IMPC:  MGI:107851
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrialDD [auth v2],
YC [auth V2]		244Mus musculusMutation(s): 0 
Gene Names: Ndufv2
EC: 7.1.1.2
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IMPC:  MGI:1920150
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialED [auth s1],
ZC [auth S1]		716Mus musculusMutation(s): 0 
Gene Names: Ndufs1
EC: 7.1.1.2
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IMPC:  MGI:2443241
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialAD [auth S7],
FD [auth s7]		224Mus musculusMutation(s): 0 
Gene Names: Ndufs7
EC: 7.1.1.2
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IMPC:  MGI:1922656
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialBD [auth S8],
GD [auth s8]		212Mus musculusMutation(s): 0 
Gene Names: Ndufs8
EC: 7.1.1.2
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IMPC:  MGI:2385079
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP
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JD [auth A9],
QD [auth a9]		NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEC
Query on HEC
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VD [auth 3D],
YD [auth 3O]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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TD [auth 3C],
UD [auth 3C],
WD [auth 3N],
XD [auth 3N]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
EHZ
Query on EHZ
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LD [auth A6],
MD [auth B9],
ND [auth 5a],
SD [auth a6]		~{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
DGT
Query on DGT
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ID [auth AL],
PD [auth al]		2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
FMN
Query on FMN
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IE [auth v1],
ZD [auth V1]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4
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AE [auth V1]
CE [auth S1]
DE [auth S1]
FE [auth S7]
GE [auth S8]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES
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BE [auth V2],
EE [auth S1],
KE [auth v2],
NE [auth s1]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN
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KD [auth S6],
RD [auth s6]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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HD [auth AL],
OD [auth al]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR		C [auth S2],
QA [auth s2]		L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME		D [auth 1],
RA [auth 1a]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM137929

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-19
    Changes: Data collection, Database references