8B6F

Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) 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
Lipid-A-disaccharide synthaseA [auth A0]516Tetrahymena thermophila SB210Mutation(s): 0 
EC: 2.4.1.182
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent epimerase/dehydratase family proteinB [auth A1]362Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DnaJ domain proteinC [auth A2]317Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase IID [auth A3]333Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNase III domain-containing proteinE [auth A4]311Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
37S ribosomal protein S25, mitochondrialF [auth A5]282Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeG [auth A6]251Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CX9C domain-containing proteinH [auth A7]238Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NDUTT15I [auth A8]217Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeJ [auth A9]231Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5K [auth AA]750Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 75 kDa subunitL [auth AB]718Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 4M [auth AC]505Tetrahymena thermophila SB210Mutation(s): 0 
EC: 7.1.1.2
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialN [auth AD]474Tetrahymena thermophila SB210Mutation(s): 0 
EC: 7.1.1.2
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 7O [auth AE]442Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf65P [auth AF]360Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor apfi protein, putativeQ [auth AG]346Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 1R [auth AH]284Tetrahymena thermophila SB210Mutation(s): 0 
EC: 7.1.1.2
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 24 kDa subunitS [auth AI]274Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf62T [auth AJ]255Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-carbonic anhydraseU [auth AK]257Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase 1, chain, putativeV [auth AL]236Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-carbonic anhydraseW [auth AM]233Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ETC complex I subunit motif proteinX [auth AN]206Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 9Y [auth AO]198Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12Z [auth AP]194Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialAA [auth AQ]189Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialBA [auth AR]185Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase, putativeCA [auth AS]172Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 10DA [auth AT]162Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase complex I, 21 kDa subunitEA [auth AU]150Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinFA [auth AV]138Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinGA [auth AW]133Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-ubiquinone oxidoreductase chain 3HA [auth AX]121Tetrahymena thermophila SB210Mutation(s): 0 
EC: 7.1.1.2
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf58IA [auth AY]116Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L51/S25/CI-B8 domain proteinJA [auth AZ]103Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeKA [auth B0]94Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit e, mitochondrialLA [auth B1]93Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
GRAM domain proteinMA [auth B2]94Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeNA [auth B3]83Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeOA [auth B4]73Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativePA [auth B5]71Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
ND1bQA [auth B6]59Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane proteinRA [auth BA]212Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for I7MIE0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeSA [auth BB]214Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB8TA [auth BC]207Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeUA [auth BD]205Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
NDUPH2VA [auth BE]189Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB10WA [auth BF]188Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
NDUA13XA [auth BG]175Tetrahymena thermophila SB210Mutation(s): 0 
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Find proteins for I7M2U4 (Tetrahymena thermophila (strain SB210))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 2YA [auth BH]178Tetrahymena thermophila SB210Mutation(s): 0 
EC: 1.6.5.3
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
2 iron, 2 sulfur cluster-binding proteinZA [auth BI]172Tetrahymena thermophila SB210Mutation(s): 0 
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Find proteins for Q22W11 (Tetrahymena thermophila (strain SB210))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
ThioredoxinAB [auth BJ]166Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
COX assembly mitochondrial proteinBB [auth BK]144Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeCB [auth BL]143Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeDB [auth BM]135Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
PH domain-containing proteinEB [auth BN]135Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8FB [auth BO]136Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for Q23B10 (Tetrahymena thermophila (strain SB210))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB6GB [auth BP]129Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4HB [auth BQ]127Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc-finger proteinIB [auth BR]132Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
Find proteins for I7MK02 (Tetrahymena thermophila (strain SB210))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB4JB [auth BS]126Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
NDUB15KB [auth BT]125Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
NDUTT16LB [auth BU]134Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
NDUTT17MB [auth BV]125Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
CHCH domain-containing proteinNB [auth BW]120Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putativeOB [auth BX]113Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Ymf57PB [auth BY]100Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Complex I-MNLLQB [auth BZ]102Tetrahymena thermophila SB210Mutation(s): 0 
UniProt
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
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AD [auth AF]
AE [auth BC]
BD [auth AF]
BE
CE [auth BG]
AD [auth AF],
AE [auth BC],
BD [auth AF],
BE,
CE [auth BG],
EE [auth BL],
KD [auth AM],
LC [auth AA],
LE [auth BT],
MD [auth AP],
NE [auth BV],
OE [auth BY],
RB [auth A0],
SB [auth A0],
SC [auth AA],
TD [auth B0],
UD [auth B0],
WC [auth AC],
WD [auth B1],
XB [auth A1],
XC [auth AC],
ZD [auth BC]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PC1
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BC [auth A2]
CD [auth AH]
DC [auth A6]
EC [auth A6]
ED [auth AJ]
BC [auth A2],
CD [auth AH],
DC [auth A6],
EC [auth A6],
ED [auth AJ],
HC [auth A9],
HE [auth BQ],
ID [auth AL],
JE [auth BS],
KC [auth A9],
KE [auth BS],
LD [auth AM],
ME [auth BT],
NC [auth AA],
OC [auth AA],
OD [auth AQ],
PC [auth AA],
PE [auth BY],
QC [auth AA],
RC [auth AA],
RD [auth AU],
SD [auth AU],
VB [auth A0],
VD [auth B1],
XD [auth B1],
YB [auth A1],
ZB [auth A1]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
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AC [auth A2]
FD [auth AJ]
GE [auth BP]
IC [auth A9]
JC [auth A9]
AC [auth A2],
FD [auth AJ],
GE [auth BP],
IC [auth A9],
JC [auth A9],
YD [auth BA]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
NDP (Subject of Investigation/LOI)
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WB [auth A1]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N