8B6F image
Deposition Date 2022-09-27
Release Date 2023-03-29
Last Version Date 2024-11-20
Entry Detail
PDB ID:
8B6F
Title:
Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) from respiratory supercomplex of Tetrahymena thermophila
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lipid-A-disaccharide synthase
Gene (Uniprot):TTHERM_00925340
Chain IDs:A (auth: A0)
Chain Length:516
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NAD-dependent epimerase/dehydratase family protein
Gene (Uniprot):TTHERM_00557760
Chain IDs:B (auth: A1)
Chain Length:362
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:DnaJ domain protein
Gene (Uniprot):TTHERM_00938750
Chain IDs:C (auth: A2)
Chain Length:317
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Gene (Uniprot):TTHERM_01000190
Chain IDs:D (auth: A3)
Chain Length:333
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:RNase III domain-containing protein
Gene (Uniprot):TTHERM_00268000
Chain IDs:E (auth: A4)
Chain Length:311
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:37S ribosomal protein S25, mitochondrial
Gene (Uniprot):TTHERM_00399360
Chain IDs:F (auth: A5)
Chain Length:282
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00697370
Chain IDs:G (auth: A6)
Chain Length:251
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:CX9C domain-containing protein
Gene (Uniprot):TTHERM_00464930
Chain IDs:H (auth: A7)
Chain Length:238
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUTT15
Chain IDs:I (auth: A8)
Chain Length:217
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00945210
Chain IDs:J (auth: A9)
Chain Length:231
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 5
Gene (Uniprot):nad5
Chain IDs:K (auth: AA)
Chain Length:750
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase 75 kDa subunit
Gene (Uniprot):TTHERM_00194260
Chain IDs:L (auth: AB)
Chain Length:718
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 4
Gene (Uniprot):nad4
Chain IDs:M (auth: AC)
Chain Length:505
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Gene (Uniprot):TTHERM_00193910
Chain IDs:N (auth: AD)
Chain Length:474
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 7
Gene (Uniprot):nad7
Chain IDs:O (auth: AE)
Chain Length:442
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf65
Gene (Uniprot):ymf65
Chain IDs:P (auth: AF)
Chain Length:360
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transcription factor apfi protein, putative
Gene (Uniprot):TTHERM_00136440
Chain IDs:Q (auth: AG)
Chain Length:346
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 1
Gene (Uniprot):nad1_a
Chain IDs:R (auth: AH)
Chain Length:284
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase 24 kDa subunit
Gene (Uniprot):TTHERM_00335630
Chain IDs:S (auth: AI)
Chain Length:274
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf62
Gene (Uniprot):ymf62
Chain IDs:T (auth: AJ)
Chain Length:255
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Gamma-carbonic anhydrase
Gene (Uniprot):TTHERM_01005010
Chain IDs:U (auth: AK)
Chain Length:257
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase 1, chain, putative
Gene (Uniprot):TTHERM_00294640
Chain IDs:V (auth: AL)
Chain Length:236
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Gamma-carbonic anhydrase
Gene (Uniprot):TTHERM_00541460
Chain IDs:W (auth: AM)
Chain Length:233
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:ETC complex I subunit motif protein
Gene (Uniprot):TTHERM_01161000
Chain IDs:X (auth: AN)
Chain Length:206
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 9
Gene (Uniprot):nad9_2
Chain IDs:Y (auth: AO)
Chain Length:198
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Gene (Uniprot):TTHERM_00194499
Chain IDs:Z (auth: AP)
Chain Length:194
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Gene (Uniprot):TTHERM_00985010
Chain IDs:AA (auth: AQ)
Chain Length:189
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Gene (Uniprot):TTHERM_00526930
Chain IDs:BA (auth: AR)
Chain Length:185
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase, putative
Gene (Uniprot):TTHERM_00933070
Chain IDs:CA (auth: AS)
Chain Length:172
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 10
Gene (Uniprot):nad10
Chain IDs:DA (auth: AT)
Chain Length:162
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
Gene (Uniprot):TTHERM_00715850
Chain IDs:EA (auth: AU)
Chain Length:150
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein
Gene (Uniprot):TTHERM_01005100
Chain IDs:FA (auth: AV)
Chain Length:138
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Acyl carrier protein
Gene (Uniprot):TTHERM_00470710
Chain IDs:GA (auth: AW)
Chain Length:133
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH-ubiquinone oxidoreductase chain 3
Gene (Uniprot):nad3
Chain IDs:HA (auth: AX)
Chain Length:121
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf58
Gene (Uniprot):ymf58
Chain IDs:IA (auth: AY)
Chain Length:116
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L51/S25/CI-B8 domain protein
Gene (Uniprot):TTHERM_00659070
Chain IDs:JA (auth: AZ)
Chain Length:103
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00455560
Chain IDs:KA (auth: B0)
Chain Length:94
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:ATP synthase subunit e, mitochondrial
Gene (Uniprot):TTHERM_00835330
Chain IDs:LA (auth: B1)
Chain Length:93
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:GRAM domain protein
Gene (Uniprot):TTHERM_000129647
Chain IDs:MA (auth: B2)
Chain Length:94
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00446569
Chain IDs:NA (auth: B3)
Chain Length:83
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00992800
Chain IDs:OA (auth: B4)
Chain Length:73
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00399460
Chain IDs:PA (auth: B5)
Chain Length:71
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:ND1b
Chain IDs:QA (auth: B6)
Chain Length:59
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein
Gene (Uniprot):TTHERM_00295430
Chain IDs:RA (auth: BA)
Chain Length:212
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00114380
Chain IDs:SA (auth: BB)
Chain Length:214
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUB8
Gene (Uniprot):TTHERM_00481330
Chain IDs:TA (auth: BC)
Chain Length:207
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00649080
Chain IDs:UA (auth: BD)
Chain Length:205
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUPH2
Gene (Uniprot):TTHERM_00193950
Chain IDs:VA (auth: BE)
Chain Length:189
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUB10
Gene (Uniprot):TTHERM_00193750
Chain IDs:WA (auth: BF)
Chain Length:188
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUA13
Gene (Uniprot):TTHERM_00149260
Chain IDs:XA (auth: BG)
Chain Length:175
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase subunit 2
Gene (Uniprot):nad2
Chain IDs:YA (auth: BH)
Chain Length:178
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:2 iron, 2 sulfur cluster-binding protein
Gene (Uniprot):TTHERM_00161210
Chain IDs:ZA (auth: BI)
Chain Length:172
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Thioredoxin
Gene (Uniprot):TTHERM_01205250
Chain IDs:AB (auth: BJ)
Chain Length:166
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COX assembly mitochondrial protein
Gene (Uniprot):TTHERM_00334340
Chain IDs:BB (auth: BK)
Chain Length:144
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00637590
Chain IDs:CB (auth: BL)
Chain Length:143
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00148710
Chain IDs:DB (auth: BM)
Chain Length:135
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:PH domain-containing protein
Gene (Uniprot):TTHERM_00006120
Chain IDs:EB (auth: BN)
Chain Length:135
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Gene (Uniprot):TTHERM_00653670
Chain IDs:FB (auth: BO)
Chain Length:136
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUB6
Gene (Uniprot):TTHERM_00430000
Chain IDs:GB (auth: BP)
Chain Length:129
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Gene (Uniprot):TTHERM_00616320
Chain IDs:HB (auth: BQ)
Chain Length:127
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Zinc-finger protein
Gene (Uniprot):TTHERM_00497570
Chain IDs:IB (auth: BR)
Chain Length:132
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUB4
Gene (Uniprot):TTHERM_00310880
Chain IDs:JB (auth: BS)
Chain Length:126
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUB15
Chain IDs:KB (auth: BT)
Chain Length:125
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUTT16
Chain IDs:LB (auth: BU)
Chain Length:134
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NDUTT17
Chain IDs:MB (auth: BV)
Chain Length:125
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:CHCH domain-containing protein
Gene (Uniprot):TTHERM_00402070
Chain IDs:NB (auth: BW)
Chain Length:120
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00185570
Chain IDs:OB (auth: BX)
Chain Length:113
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf57
Gene (Uniprot):ymf57
Chain IDs:PB (auth: BY)
Chain Length:100
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Complex I-MNLL
Gene (Uniprot):TTHERM_00160690
Chain IDs:QB (auth: BZ)
Chain Length:102
Number of Molecules:1
Biological Source:Tetrahymena thermophila SB210
Primary Citation
Structural basis of mitochondrial membrane bending by the I-II-III 2 -IV 2 supercomplex.
Nature 615 934 938 (2023)
PMID: 36949187 DOI: 10.1038/s41586-023-05817-y

Abstact

Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. 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-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.

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Primary Citation of related structures