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- PDB-8b6h: Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from... -

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Basic information

Entry
Database: PDB / ID: 8b6h
TitleCryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila
Components
  • (Cytochrome c oxidase subunit ...) x 3
  • (NADH dehydrogenase [ubiquinone] 1 ...) x 2
  • (SURF1-like protein) x 2
  • (Transmembrane protein, ...) x 12
  • (Zf-Tim10_DDP domain-containing ...) x 2
  • 2-oxoglutarate/malate carrier protein
  • 39S ribosomal protein L9, mitochondrial
  • ABC transporter
  • Annexin
  • COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein
  • COXTT10
  • COXTT12,Transmembrane protein,Transmembrane protein
  • COXTT22
  • COXTT27
  • COXTT28
  • COXTT9
  • CTF/NF-I domain-containing protein
  • Carrier protein
  • Complex III subunit VII
  • Cullin domain-containing protein
  • Decapping nuclease
  • Iron-binding zinc finger CDGSH type protein
  • Lysozyme
  • Mobilization protein
  • Oxoglutarate/malate translocator protein, putative
  • Phage protein
  • Protein phosphatase 2C, putative
  • Structural protein
  • Tim10/DDP family zinc finger protein
  • TraB family protein
  • Transmembrane protein
  • Transposase
  • YflT domain-containing protein
  • Ymf67
  • Ymf68
  • Ymf70
  • Ymf75
KeywordsELECTRON TRANSPORT / Ciliate / mitochondrial / supercomplex
Function / homology
Function and homology information


dicarboxylic acid transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / : / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport ...dicarboxylic acid transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / : / cytochrome-c oxidase / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport / mitochondrial inner membrane / copper ion binding / DNA-binding transcription factor activity / heme binding / mitochondrion / membrane / nucleus / metal ion binding
Similarity search - Function
Surfeit locus 1/Shy1 / Surfeit locus 1/4 / TraB/PryY-like / SURF1 family / SURF1 family profile. / CTF transcription factor/nuclear factor 1, DNA-binding domain / CTF/NF-I DNA-binding domain profile. / : / Tim10-like / Tim10-like domain superfamily ...Surfeit locus 1/Shy1 / Surfeit locus 1/4 / TraB/PryY-like / SURF1 family / SURF1 family profile. / CTF transcription factor/nuclear factor 1, DNA-binding domain / CTF/NF-I DNA-binding domain profile. / : / Tim10-like / Tim10-like domain superfamily / : / Tim10/DDP family zinc finger / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown. / : / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxin / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-LPP ...1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-LPP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ubiquinone-8 / Oxoglutarate/malate translocator protein, putative / Transmembrane protein / SURF1-like protein / Uncharacterized protein / Transmembrane protein / Transmembrane protein, putative / SURF1-like protein / Transmembrane protein / Iron-binding zinc finger CDGSH type protein / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein / Uncharacterized protein / CTF/NF-I domain-containing protein / Transmembrane protein, putative / Protein phosphatase 2C, putative / Uncharacterized protein / Transmembrane protein, putative / Chromosome condensation regulator RCC1 repeat protein / Transmembrane protein, putative / Carrier protein / Uncharacterized protein / Tim10/DDP family zinc finger protein / Uncharacterized protein / Transmembrane protein, putative / Transmembrane protein, putative / TraB family protein / Transmembrane protein, putative / Uncharacterized protein / Uncharacterized protein / Cytochrome C oxidase subunit Vb protein / 2-oxoglutarate/malate carrier protein / Transmembrane protein, putative / Transmembrane protein, putative / Uncharacterized protein / Uncharacterized protein / Ymf70 / Cytochrome c oxidase subunit 1 / Ymf68 / Ymf67 / Cytochrome c oxidase polypeptide II / Ymf75 / Transmembrane protein, putative / Transmembrane protein / Mitochondrial import inner membrane translocase subunit / Uncharacterized protein / Transmembrane protein, putative / Tim10/DDP family zinc finger protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Cancerfonden2017/1041 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Citation
Journal: Nature / Year: 2023
Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts /
Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. 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-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Authors: Muhleip, A. / Flygaard, R.K. / Haapanen, O. / Baradaran, R. / Gruhl, T. / Tobiasson, V. / Marechal, A. / Sharma, V. / Amunts, A.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
DA: Cytochrome c oxidase subunit 1
DB: Cytochrome c oxidase subunit 2
DC: Ymf68
DD: Cytochrome C oxidase subunit Vb protein
DE: Transmembrane protein, putative
DF: Structural protein
DG: Transmembrane protein, putative
DH: Transmembrane protein, putative
DI: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
DJ: Transmembrane protein, putative
DK: CTF/NF-I domain-containing protein
DM: Transmembrane protein, putative
DN: Ymf67
DO: Protein phosphatase 2C, putative
DP: SURF1-like protein
DQ: TraB family protein
DR: Transmembrane protein, putative
DS: Oxoglutarate/malate translocator protein, putative
DT: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial
DU: Carrier protein
DV: 2-oxoglutarate/malate carrier protein
DW: SURF1-like protein
DX: COXTT9
DY: COXTT10
DZ: 39S ribosomal protein L9, mitochondrial
EA: COXTT12,Transmembrane protein,Transmembrane protein
EB: Transmembrane protein, putative
EC: COXTT27
ED: Ymf75
EE: Mobilization protein
EF: Iron-binding zinc finger CDGSH type protein
EG: COXTT28
EH: Transmembrane protein, putative
EI: Transmembrane protein
EV: Decapping nuclease
EK: Complex III subunit VII
EL: Transmembrane protein, putative
EM: Transmembrane protein, putative
EN: COXTT22
EO: Transmembrane protein, putative
EP: Phage protein
EQ: Transmembrane protein, putative
ER: Lysozyme
ES: Ymf70
ET: Zf-Tim10_DDP domain-containing protein
EU: ABC transporter
EJ: YflT domain-containing protein
EW: Cullin domain-containing protein
EX: Zf-Tim10_DDP domain-containing protein
EY: Annexin
EZ: Transposase
FA: Tim10/DDP family zinc finger protein
Da: Cytochrome c oxidase subunit 1
Db: Cytochrome c oxidase subunit 2
Dc: Ymf68
Dd: Cytochrome C oxidase subunit Vb protein
De: Transmembrane protein, putative
Df: Structural protein
Dg: Transmembrane protein, putative
Dh: Transmembrane protein, putative
Di: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Dj: Transmembrane protein, putative
Dk: CTF/NF-I domain-containing protein
Dm: Transmembrane protein, putative
Dn: Ymf67
Do: Protein phosphatase 2C, putative
Dp: SURF1-like protein
Dq: TraB family protein
Dr: Transmembrane protein, putative
Ds: Oxoglutarate/malate translocator protein, putative
Dt: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial
Du: Carrier protein
Dv: 2-oxoglutarate/malate carrier protein
Dw: SURF1-like protein
Dx: COXTT9
Dy: COXTT10
Dz: 39S ribosomal protein L9, mitochondrial
Ea: COXTT12,Transmembrane protein,Transmembrane protein
Eb: Transmembrane protein, putative
Ec: COXTT27
Ed: Ymf75
Ee: Mobilization protein
Ef: Iron-binding zinc finger CDGSH type protein
Eg: COXTT28
Eh: Transmembrane protein, putative
Ei: Transmembrane protein
Ev: Decapping nuclease
Ek: Complex III subunit VII
El: Transmembrane protein, putative
Em: Transmembrane protein, putative
En: COXTT22
Eo: Transmembrane protein, putative
Ep: Phage protein
Eq: Transmembrane protein, putative
Er: Lysozyme
Es: Ymf70
Et: Zf-Tim10_DDP domain-containing protein
Eu: ABC transporter
Ej: YflT domain-containing protein
Ew: Cullin domain-containing protein
Ex: Zf-Tim10_DDP domain-containing protein
Ey: Annexin
Ez: Transposase
Fa: Tim10/DDP family zinc finger protein
Dl: COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein
DL: COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,468,231351
Polymers3,209,322106
Non-polymers258,909245
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome c oxidase subunit ... , 3 types, 6 molecules DADaDBDbDDDd

#1: Protein Cytochrome c oxidase subunit 1


Mass: 80578.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y4
#2: Protein Cytochrome c oxidase subunit 2


Mass: 72388.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y9
#4: Protein Cytochrome C oxidase subunit Vb protein


Mass: 75431.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23FF5

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Protein , 34 types, 68 molecules DCDcDFDfDKDkDNDnDODoDPDpDQDqDSDsDUDuDVDvDWDwDXDxDYDyDZDzEAEa...

#3: Protein Ymf68


Mass: 72782.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y6
#6: Protein Structural protein


Mass: 27946.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q24I72
#11: Protein CTF/NF-I domain-containing protein


Mass: 116812.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22CI1
#13: Protein Ymf67


Mass: 54538.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y7
#14: Protein Protein phosphatase 2C, putative


Mass: 53011.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22FX8
#15: Protein SURF1-like protein


Mass: 47087.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7M1Q4
#16: Protein TraB family protein


Mass: 45064.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23DP7
#18: Protein Oxoglutarate/malate translocator protein, putative


Mass: 40434.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: A4VDV3
#20: Protein Carrier protein


Mass: 37095.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22ZA6
#21: Protein 2-oxoglutarate/malate carrier protein


Mass: 36132.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23M99
#22: Protein SURF1-like protein


Mass: 35794.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7LTZ4
#23: Protein COXTT9


Mass: 29865.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7LY65
#24: Protein COXTT10


Mass: 28101.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7MD70
#25: Protein 39S ribosomal protein L9, mitochondrial


Mass: 27034.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7X4J9
#26: Protein COXTT12,Transmembrane protein,Transmembrane protein


Mass: 25953.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7M3P9
#28: Protein COXTT27


Mass: 23368.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#29: Protein Ymf75


Mass: 23325.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q951A7
#30: Protein Mobilization protein


Mass: 23257.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23F08
#31: Protein Iron-binding zinc finger CDGSH type protein


Mass: 21476.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7M8P0
#32: Protein COXTT28


Mass: 11121.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#34: Protein Transmembrane protein


Mass: 20025.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7MKT6
#35: Protein Decapping nuclease


Mass: 10242.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7LVX0
#36: Protein Complex III subunit VII


Mass: 19882.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q230X6
#39: Protein COXTT22


Mass: 17701.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7MFV5
#41: Protein Phage protein


Mass: 14740.897 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q24C97
#43: Protein Lysozyme


Mass: 12273.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7M9E7
#44: Protein Ymf70


Mass: 10891.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y0
#46: Protein ABC transporter


Mass: 10418.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7LTF1
#47: Protein YflT domain-containing protein


Mass: 19979.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7M8Y9
#48: Protein Cullin domain-containing protein


Mass: 8965.917 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22N23
#50: Protein Annexin


Mass: 8155.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q233U0
#51: Protein Transposase


Mass: 8081.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22A35
#52: Protein Tim10/DDP family zinc finger protein


Mass: 8008.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7X3D6
#53: Protein COXBP,Chromosome condensation regulator RCC1 repeat protein,Chromosome condensation regulator RCC1 repeat protein


Mass: 58697.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22RF2

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Transmembrane protein, ... , 12 types, 24 molecules DEDeDGDgDHDhDJDjDMDmDRDrEBEbEHEhELElEMEmEOEoEQEq

#5: Protein Transmembrane protein, putative


Mass: 15618.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7XCY5
#7: Protein Transmembrane protein, putative


Mass: 12786.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23DS4
#8: Protein Transmembrane protein, putative


Mass: 16427.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7MGF9
#10: Protein Transmembrane protein, putative


Mass: 26601.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7WZP1
#12: Protein Transmembrane protein, putative


Mass: 57814.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22PJ5
#17: Protein Transmembrane protein, putative


Mass: 41307.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23DG8
#27: Protein Transmembrane protein, putative


Mass: 24701.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: I7LZX8
#33: Protein Transmembrane protein, putative


Mass: 20388.264 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23D87
#37: Protein Transmembrane protein, putative


Mass: 18801.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23VY4
#38: Protein Transmembrane protein, putative


Mass: 18600.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22DP8
#40: Protein Transmembrane protein, putative


Mass: 15588.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23TE5
#42: Protein Transmembrane protein, putative


Mass: 14344.524 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q22W32

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NADH dehydrogenase [ubiquinone] 1 ... , 2 types, 4 molecules DIDiDTDt

#9: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 28666.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7X287
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8, mitochondrial


Mass: 37552.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q23DZ5

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Zf-Tim10 DDP domain-containing ... , 2 types, 4 molecules ETEtEXEx

#45: Protein Zf-Tim10_DDP domain-containing protein


Mass: 10435.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q231A8
#49: Protein Zf-Tim10_DDP domain-containing protein


Mass: 8354.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: W7XDM6

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Non-polymers , 15 types, 245 molecules

#54: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#56: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#57: Chemical...
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 118 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#58: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#59: Chemical...
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#60: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#61: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#63: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#64: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#65: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#66: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#67: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#68: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cytochrome c oxidase dimer (complex-IV) from respiratory supercomplex of Tetrahymena thermophila
Type: COMPLEX / Entity ID: #1-#53 / Source: NATURAL
Molecular weightValue: 3.2 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 25.66 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002220544
ELECTRON MICROSCOPYf_angle_d0.462295092
ELECTRON MICROSCOPYf_dihedral_angle_d10.44486984
ELECTRON MICROSCOPYf_chiral_restr0.05929348
ELECTRON MICROSCOPYf_plane_restr0.00336004

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