8B6H image
Deposition Date 2022-09-27
Release Date 2023-03-29
Last Version Date 2023-04-12
Entry Detail
PDB ID:
8B6H
Title:
Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):cox1
Chain IDs:A (auth: DA), AB (auth: Da)
Chain Length:688
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):cox2
Chain IDs:B (auth: DB), BB (auth: Db)
Chain Length:604
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf68
Gene (Uniprot):ymf68
Chain IDs:C (auth: DC), CB (auth: Dc)
Chain Length:594
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Cytochrome C oxidase subunit Vb protein
Gene (Uniprot):TTHERM_00378620
Chain IDs:D (auth: DD), DB (auth: Dd)
Chain Length:637
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_000723218
Chain IDs:E (auth: DE), EB (auth: De)
Chain Length:130
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Structural protein
Gene (Uniprot):TTHERM_00568030
Chain IDs:F (auth: DF), FB (auth: Df)
Chain Length:230
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00046170
Chain IDs:G (auth: DG), GB (auth: Dg)
Chain Length:103
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00151250
Chain IDs:H (auth: DH), HB (auth: Dh)
Chain Length:133
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Gene (Uniprot):TTHERM_000470561
Chain IDs:I (auth: DI), IB (auth: Di)
Chain Length:236
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_001001528
Chain IDs:J (auth: DJ), JB (auth: Dj)
Chain Length:220
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:CTF/NF-I domain-containing protein
Gene (Uniprot):TTHERM_01043280
Chain IDs:K (auth: DK), KB (auth: Dk)
Chain Length:990
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00361490
Chain IDs:L (auth: DM), LB (auth: Dm)
Chain Length:490
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf67
Gene (Uniprot):ymf67
Chain IDs:M (auth: DN), MB (auth: Dn)
Chain Length:453
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Protein phosphatase 2C, putative
Gene (Uniprot):TTHERM_00721790
Chain IDs:N (auth: DO), NB (auth: Do)
Chain Length:473
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:SURF1-like protein
Gene (Uniprot):TTHERM_00338280
Chain IDs:O (auth: DP), OB (auth: Dp)
Chain Length:402
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:TraB family protein
Gene (Uniprot):TTHERM_00046440
Chain IDs:P (auth: DQ), PB (auth: Dq)
Chain Length:385
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00047230
Chain IDs:Q (auth: DR), QB (auth: Dr)
Chain Length:348
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Oxoglutarate/malate translocator protein, putative
Gene (Uniprot):TTHERM_00127269
Chain IDs:R (auth: DS), RB (auth: Ds)
Chain Length:346
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial
Gene (Uniprot):TTHERM_00675650
Chain IDs:S (auth: DT), SB (auth: Dt)
Chain Length:318
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Carrier protein
Gene (Uniprot):TTHERM_00112650
Chain IDs:T (auth: DU), TB (auth: Du)
Chain Length:330
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:2-oxoglutarate/malate carrier protein
Gene (Uniprot):TTHERM_00621600
Chain IDs:U (auth: DV), UB (auth: Dv)
Chain Length:318
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:SURF1-like protein
Gene (Uniprot):TTHERM_00070850
Chain IDs:V (auth: DW), VB (auth: Dw)
Chain Length:318
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT9
Gene (Uniprot):TTHERM_00525160
Chain IDs:W (auth: DX), WB (auth: Dx)
Chain Length:252
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT10
Gene (Uniprot):TTHERM_00420130
Chain IDs:X (auth: DY), XB (auth: Dy)
Chain Length:234
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:39S ribosomal protein L9, mitochondrial
Gene (Uniprot):TTHERM_000939159
Chain IDs:Y (auth: DZ), YB (auth: Dz)
Chain Length:231
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein
Gene (Uniprot):TTHERM_00016360
Chain IDs:AD (auth: Dl), BD (auth: DL)
Chain Length:536
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT12,Transmembrane protein,Transmembrane protein
Gene (Uniprot):TTHERM_00455090
Chain IDs:Z (auth: EA), ZB (auth: Ea)
Chain Length:215
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00530650
Chain IDs:AA (auth: EB), AC (auth: Eb)
Chain Length:210
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT27
Chain IDs:BA (auth: EC), BC (auth: Ec)
Chain Length:212
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf75
Gene (Uniprot):ymf75
Chain IDs:CA (auth: ED), CC (auth: Ed)
Chain Length:190
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Mobilization protein
Gene (Uniprot):TTHERM_00641250
Chain IDs:DA (auth: EE), DC (auth: Ee)
Chain Length:193
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Iron-binding zinc finger CDGSH type protein
Gene (Uniprot):TTHERM_00133510
Chain IDs:EA (auth: EF), EC (auth: Ef)
Chain Length:188
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT28
Chain IDs:FA (auth: EG), FC (auth: Eg)
Chain Length:100
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00049040
Chain IDs:GA (auth: EH), GC (auth: Eh)
Chain Length:173
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein
Gene (Uniprot):TTHERM_00218570
Chain IDs:HA (auth: EI), HC (auth: Ei)
Chain Length:173
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:YflT domain-containing protein
Gene (Uniprot):TTHERM_00218840
Chain IDs:UA (auth: EJ), UC (auth: Ej)
Chain Length:175
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Complex III subunit VII
Gene (Uniprot):TTHERM_00433830
Chain IDs:JA (auth: EK), JC (auth: Ek)
Chain Length:170
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00794470
Chain IDs:KA (auth: EL), KC (auth: El)
Chain Length:158
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00938940
Chain IDs:LA (auth: EM), LC (auth: Em)
Chain Length:154
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:COXTT22
Gene (Uniprot):TTHERM_00691100
Chain IDs:MA (auth: EN), MC (auth: En)
Chain Length:149
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00666370
Chain IDs:NA (auth: EO), NC (auth: Eo)
Chain Length:124
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Phage protein
Gene (Uniprot):TTHERM_00695750
Chain IDs:OA (auth: EP), OC (auth: Ep)
Chain Length:127
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transmembrane protein, putative
Gene (Uniprot):TTHERM_00161000
Chain IDs:PA (auth: EQ), PC (auth: Eq)
Chain Length:122
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Lysozyme
Gene (Uniprot):TTHERM_00151580
Chain IDs:QA (auth: ER), QC (auth: Er)
Chain Length:105
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Ymf70
Gene (Uniprot):ymf70
Chain IDs:RA (auth: ES), RC (auth: Es)
Chain Length:89
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Zf-Tim10_DDP domain-containing protein
Gene (Uniprot):TTHERM_00433490
Chain IDs:SA (auth: ET), SC (auth: Et)
Chain Length:93
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:ABC transporter
Gene (Uniprot):TTHERM_00485790
Chain IDs:TA (auth: EU), TC (auth: Eu)
Chain Length:90
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Decapping nuclease
Gene (Uniprot):TTHERM_00218340
Chain IDs:IA (auth: EV), IC (auth: Ev)
Chain Length:88
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Cullin domain-containing protein
Gene (Uniprot):TTHERM_00028510
Chain IDs:VA (auth: EW), VC (auth: Ew)
Chain Length:81
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Zf-Tim10_DDP domain-containing protein
Gene (Uniprot):TTHERM_000703379
Chain IDs:WA (auth: EX), WC (auth: Ex)
Chain Length:72
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Annexin
Gene (Uniprot):TTHERM_00805850
Chain IDs:XA (auth: EY), XC (auth: Ey)
Chain Length:72
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Transposase
Gene (Uniprot):TTHERM_01289060
Chain IDs:YA (auth: EZ), YC (auth: Ez)
Chain Length:68
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Polymer Type:polypeptide(L)
Molecule:Tim10/DDP family zinc finger protein
Gene (Uniprot):TTHERM_000528460
Chain IDs:ZA (auth: FA), ZC (auth: Fa)
Chain Length:72
Number of Molecules:2
Biological Source:Tetrahymena thermophila SB210
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AME H MET modified residue
SEP D SER modified residue
TPO D THR modified residue
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures