8B6J

Cryo-EM structure of cytochrome bc1 complex (complex-III) from respiratory supercomplex of Tetrahymena thermophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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
Peptidase M16 inactive domain proteinA,
L [auth a]
513Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for I7MGU2 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MGU2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M16 family peptidase, putativeB,
M [auth b]
482Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for I7MJ25 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MJ25
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome bC,
N [auth c]
426Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for Q950Z1 (Tetrahymena thermophila)
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UniProt GroupQ950Z1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome protein c1D,
O [auth d]
319Tetrahymena thermophila SB210Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q24IM5 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ24IM5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske iron-sulfur protein, ubiquinol-cytochrome C reductase iron-sulfur subunitE,
P [auth e]
269Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for I7MIC7 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MIC7
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase hinge proteinF,
Q [auth f]
86Tetrahymena thermophila SB210Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q23K66 (Tetrahymena thermophila (strain SB210))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRTT1G,
R [auth g]
328Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for Q23F81 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ23F81
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeH,
S [auth h]
130Tetrahymena thermophila SB210Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7M484 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7M484
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeI,
T [auth i]
119Tetrahymena thermophila SB210Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7MM45 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MM45
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRTT3/UP1J,
U [auth j]
66Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeK,
V [auth k]
62Tetrahymena thermophila SB210Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7MFL6 (Tetrahymena thermophila (strain SB210))
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UniProt GroupI7MFL6
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
UQCRTT2W [auth l],
X [auth L]
41Tetrahymena thermophila SB210Mutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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CA [auth C]
CB [auth c]
DA [auth C]
EA [auth C]
EB [auth c]
CA [auth C],
CB [auth c],
DA [auth C],
EA [auth C],
EB [auth c],
FA [auth C],
JB [auth g],
LB [auth h],
MB [auth h],
NA [auth D],
RA [auth E],
SA [auth H],
TA [auth H],
VA [auth a],
YA [auth c]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
Query on PC1

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AB [auth c]
BB [auth c]
FB [auth c]
GA [auth C]
GB [auth d]
AB [auth c],
BB [auth c],
FB [auth c],
GA [auth C],
GB [auth d],
HA [auth C],
IA [auth C],
KB [auth g],
NB [auth k],
PA [auth E],
QA [auth E],
UA [auth K],
Y [auth A],
Z [auth A],
ZA [auth c]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PEE
Query on PEE

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LA [auth C],
OB [auth L]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
UQ8 (Subject of Investigation/LOI)
Query on UQ8

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DB [auth c],
JA [auth C],
KA [auth C]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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HB [auth d],
MA [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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AA [auth C],
BA [auth C],
WA [auth c],
XA [auth c]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES (Subject of Investigation/LOI)
Query on FES

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IB [auth e],
OA [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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