8B6G

Cryo-EM structure of succinate dehydrogenase complex (complex-II) in respiratory supercomplex of Tetrahymena thermophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 mitochondrial membrane bending by the I-II-III 2 -IV 2 supercomplex.

Muhleip, A.Flygaard, R.K.Baradaran, R.Haapanen, O.Gruhl, T.Tobiasson, V.Marechal, A.Sharma, V.Amunts, A.

(2023) Nature 615: 934-938

  • DOI: https://doi.org/10.1038/s41586-023-05817-y
  • Primary Citation of Related Structures:  
    8B6F, 8B6G, 8B6H, 8B6J

  • PubMed Abstract: 

    Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane 1 . Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III 2 -IV 2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphthamide synthesis proteinA [auth CH]195Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7LX66 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7LX66
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeB [auth CM]76Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q22HD6 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ22HD6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TransposaseC [auth CL]89Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for W7XBF5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrialD [auth CA]636Tetrahymena thermophilaMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q23DI3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4885 domain-containing proteinE [auth CI]114Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q22YL0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase (quinone)F [auth CB]312Tetrahymena thermophilaMutation(s): 0 
EC: 1.3.5.1
UniProt
Find proteins for I7M403 (Tetrahymena thermophila (strain SB210))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeG [auth CF]296Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q248F8 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ248F8
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SDHTT3H [auth CG]198Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeI [auth CK]93Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q24CW6 (Tetrahymena thermophila (strain SB210))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NmrA domain-containing proteinJ [auth CE]322Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q24I09 (Tetrahymena thermophila (strain SB210))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeK [auth CJ]103Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q23S01 (Tetrahymena thermophila (strain SB210))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeL [auth CN]62Tetrahymena thermophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for W7XF00 (Tetrahymena thermophila (strain SB210))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8M [auth CC]60Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q23RH8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
SDHTT11N [auth CO]43Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
SDHDO [auth CD]44Tetrahymena thermophilaMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BA [auth CJ]
FA [auth CO]
GA [auth CD]
P [auth CM]
W [auth CG]
BA [auth CJ],
FA [auth CO],
GA [auth CD],
P [auth CM],
W [auth CG],
X [auth CG],
Z [auth CK]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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DA [auth CC]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
FAD (Subject of Investigation/LOI)
Query on FAD

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R [auth CA]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
3PE
Query on 3PE

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CA [auth CC],
HA [auth CD],
Y [auth CK]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
UQ8 (Subject of Investigation/LOI)
Query on UQ8

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EA [auth CC]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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AA [auth CE]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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T [auth CB]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S (Subject of Investigation/LOI)
Query on F3S

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U [auth CB]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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S [auth CB]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA

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Q [auth CA],
V [auth CB]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Swedish Foundation for Strategic ResearchSwedenFFL15:0325
CancerfondenSweden2017/1041
European Research Council (ERC)European UnionERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-04-12
    Changes: Database references