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- PDB-7w5z: Cryo-EM structure of Tetrahymena thermophila mitochondrial comple... -

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Basic information

Entry
Database: PDB / ID: 7w5z
TitleCryo-EM structure of Tetrahymena thermophila mitochondrial complex IV, composite dimer model
Components
  • (Cytochrome c oxidase small TIM subunit ...) x 5
  • (Cytochrome c oxidase subunit ...) x 18
  • (SURF1-like protein) x 2
  • (Transmembrane protein, ...) x 13
  • (Unknown peptide) x 3
  • 2-oxoglutarate/malate carrier protein
  • CTF/NF-I domain-containing protein
  • Carrier protein
  • Chromosome condensation regulator RCC1 repeat protein
  • Cyclic nucleotide-binding domain protein
  • Cytochrome c oxidase acyl carrier-like subunit
  • Iron-binding zinc finger CDGSH type protein
  • Oxoglutarate/malate translocator protein, putative
  • Protein phosphatase 2C, putative
  • Protein transporter Sec61 alpha subunit
  • Tim10/DDP family zinc finger protein
  • TraB family protein
  • Uncharacterized protein
  • Ymf67
  • Ymf68
  • Ymf70
  • Ymf75
KeywordsELECTRON TRANSPORT / cytochrome c oxidase / mitochondrial carrier / membrane complex
Function / homology
Function and homology information


thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase ...thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase / antiporter activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Golgi organization / transmembrane transporter activity / endoplasmic reticulum-Golgi intermediate compartment / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport / monoatomic ion channel activity / nucleic acid binding / mitochondrial inner membrane / membrane => GO:0016020 / copper ion binding / DNA-binding transcription factor activity / heme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / membrane / nucleus / metal ion binding
Similarity search - Function
Protein of unknown function DUF4441 / Domain of unknown function (DUF4441) / 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 ...Protein of unknown function DUF4441 / Domain of unknown function (DUF4441) / 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 / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Protein secY signature 1. / Protein secY signature 2. / 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. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / 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. / Pectin lyase fold/virulence factor / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Cupredoxin / Ion transport domain / Ion transport protein / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cyclic nucleotide-binding domain protein / Oxoglutarate/malate translocator protein, putative / Transmembrane protein / SURF1-like protein / Uncharacterized protein ...CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cyclic nucleotide-binding domain protein / 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 / Transmembrane protein, putative / 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 / 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 / Protein transporter Sec61 alpha subunit
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZhou, L. / Maldonado, M. / Padavannil, A. / Letts, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM137929 United States
CitationJournal: Science / Year: 2022
Title: Structures of 's respiratory chain reveal the diversity of eukaryotic core metabolism.
Authors: Long Zhou / María Maldonado / Abhilash Padavannil / Fei Guo / James A Letts /
Abstract: Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and ...Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII (Tt-SC I+III) and a structure of Tt-CIV. Tt-SC I+III (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM8-TIM13-like domain. Our structural and functional study of the respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U1: Unknown peptide
U2: Transmembrane protein, putative
U3: Unknown peptide
U4: Unknown peptide
U5: Uncharacterized protein
U6: Protein transporter Sec61 alpha subunit
C1: Cytochrome c oxidase subunit 1
C2: Cytochrome c oxidase subunit 2
C3: Ymf68
5B: Cytochrome C oxidase subunit Vb protein
6A: Transmembrane protein, putative
6B: Cytochrome c oxidase subunit 6B
6L: Cytochrome c oxidase subunit 6B-like
6C: Transmembrane protein, putative
7A: Transmembrane protein, putative
7C: Cytochrome c oxidase subunit 7C
7L: CTF/NF-I domain-containing protein
M1: Oxoglutarate/malate translocator protein, putative
M2: 2-oxoglutarate/malate carrier protein
M3: Carrier protein
T1: Tim10/DDP family zinc finger protein
T2: Cytochrome c oxidase small TIM subunit 2
T3: Cytochrome c oxidase small TIM subunit 3
T4: Cytochrome c oxidase small TIM subunit 4
T5: Cytochrome c oxidase small TIM subunit 5
T6: Cytochrome c oxidase small TIM subunit 6
BP: Chromosome condensation regulator RCC1 repeat protein
FS: Iron-binding zinc finger CDGSH type protein
AC: Cytochrome c oxidase acyl carrier-like subunit
Y7: Ymf67
Y0: Ymf70
Y5: Ymf75
A: Transmembrane protein, putative
B: Protein phosphatase 2C, putative
C: Cyclic nucleotide-binding domain protein
D: SURF1-like protein
E: TraB family protein
F: Transmembrane protein, putative
G: Cytochrome c oxidase subunit TT7
H: SURF1-like protein
I: Cytochrome c oxidase subunit TT9
J: Cytochrome c oxidase subunit TT10
K: Cytochrome c oxidase subunit TT11
L: Cytochrome c oxidase subunit TT12
M: Transmembrane protein, putative
N: Transmembrane protein, putative
O: Cytochrome c oxidase subunit TT15
P: Cytochrome c oxidase subunit TT16
Q: Transmembrane protein, putative
R: Cytochrome c oxidase subunit TT18
S: Cytochrome c oxidase subunit TT19
T: Transmembrane protein, putative
U: Transmembrane protein, putative
V: Cytochrome c oxidase subunit TT22
W: Transmembrane protein, putative
X: Transmembrane protein, putative
Y: Cytochrome c oxidase subunit TT25
Z: Cytochrome c oxidase subunit TT26
u1: Unknown peptide
u2: Transmembrane protein, putative
u3: Unknown peptide
u4: Unknown peptide
u5: Uncharacterized protein
u6: Protein transporter Sec61 alpha subunit
c1: Cytochrome c oxidase subunit 1
c2: Cytochrome c oxidase subunit 2
c3: Ymf68
5b: Cytochrome C oxidase subunit Vb protein
6a: Transmembrane protein, putative
6b: Cytochrome c oxidase subunit 6B
6l: Cytochrome c oxidase subunit 6B-like
6c: Transmembrane protein, putative
7a: Transmembrane protein, putative
7c: Cytochrome c oxidase subunit 7C
7l: CTF/NF-I domain-containing protein
m1: Oxoglutarate/malate translocator protein, putative
m2: 2-oxoglutarate/malate carrier protein
m3: Carrier protein
t1: Tim10/DDP family zinc finger protein
t2: Cytochrome c oxidase small TIM subunit 2
t3: Cytochrome c oxidase small TIM subunit 3
t4: Cytochrome c oxidase small TIM subunit 4
t5: Cytochrome c oxidase small TIM subunit 5
t6: Cytochrome c oxidase small TIM subunit 6
bp: Chromosome condensation regulator RCC1 repeat protein
fs: Iron-binding zinc finger CDGSH type protein
ac: Cytochrome c oxidase acyl carrier-like subunit
y7: Ymf67
y0: Ymf70
y5: Ymf75
a: Transmembrane protein, putative
b: Protein phosphatase 2C, putative
d: SURF1-like protein
e: TraB family protein
f: Transmembrane protein, putative
g: Cytochrome c oxidase subunit TT7
h: SURF1-like protein
i: Cytochrome c oxidase subunit TT9
j: Cytochrome c oxidase subunit TT10
k: Cytochrome c oxidase subunit TT11
l: Cytochrome c oxidase subunit TT12
m: Transmembrane protein, putative
n: Transmembrane protein, putative
o: Cytochrome c oxidase subunit TT15
p: Cytochrome c oxidase subunit TT16
q: Transmembrane protein, putative
r: Cytochrome c oxidase subunit TT18
s: Cytochrome c oxidase subunit TT19
t: Transmembrane protein, putative
u: Transmembrane protein, putative
v: Cytochrome c oxidase subunit TT22
w: Transmembrane protein, putative
x: Transmembrane protein, putative
y: Cytochrome c oxidase subunit TT25
z: Cytochrome c oxidase subunit TT26
c: Cyclic nucleotide-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,593,537238
Polymers4,462,311116
Non-polymers131,226122
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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Protein , 20 types, 40 molecules U1u1U5u5U6u6C3c37L7lM1m1M2m2M3m3T1t1BPbpFSfsACacY7y7Y0y0Y5y5...

#1: Protein Unknown peptide


Mass: 8358.294 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB255
#5: Protein Uncharacterized protein


Mass: 20909.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23FE4
#6: Protein Protein transporter Sec61 alpha subunit


Mass: 53674.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7XHC8
#9: Protein Ymf68


Mass: 72782.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q950Y6
#17: 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 (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22CI1
#18: Protein Oxoglutarate/malate translocator protein, putative


Mass: 40392.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: A4VDV3
#19: Protein 2-oxoglutarate/malate carrier protein


Mass: 36118.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23M99
#20: Protein Carrier protein


Mass: 37095.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22ZA6
#21: 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 (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7X3D6
#27: Protein Chromosome condensation regulator RCC1 repeat protein


Mass: 41202.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22RF2
#28: 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 (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7M8P0
#29: Protein Cytochrome c oxidase acyl carrier-like subunit


Mass: 14740.897 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q24C97
#30: Protein Ymf67


Mass: 54538.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q950Y7
#31: Protein Ymf70


Mass: 10919.931 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q950Y0
#32: Protein Ymf75


Mass: 23325.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q951A7
#34: Protein Protein phosphatase 2C, putative


Mass: 53011.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22FX8
#35: Protein Cyclic nucleotide-binding domain protein


Mass: 172272.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: A4VCQ2
#36: Protein SURF1-like protein


Mass: 47087.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7M1Q4
#37: Protein TraB family protein


Mass: 45050.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23DP7
#40: Protein SURF1-like protein


Mass: 35794.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7LTZ4

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Transmembrane protein, ... , 13 types, 26 molecules U2u26A6a6C6c7A7aAaFfMmNnQqTtUuWwXx

#2: Protein Transmembrane protein, putative


Mass: 417001.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22C06
#11: Protein Transmembrane protein, putative


Mass: 15618.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7XCY5
#14: Protein Transmembrane protein, putative


Mass: 12786.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23DS4
#15: Protein Transmembrane protein, putative


Mass: 16413.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7MGF9
#33: Protein Transmembrane protein, putative


Mass: 57814.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22PJ5
#38: Protein Transmembrane protein, putative


Mass: 41307.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23DG8
#45: Protein Transmembrane protein, putative


Mass: 26601.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7WZP1
#46: Protein Transmembrane protein, putative


Mass: 24701.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7LZX8
#49: Protein Transmembrane protein, putative


Mass: 20346.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23D87
#52: Protein Transmembrane protein, putative


Mass: 18801.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23VY4
#53: Protein Transmembrane protein, putative


Mass: 18600.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22DP8
#55: Protein Transmembrane protein, putative


Mass: 15588.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23TE5
#56: Protein Transmembrane protein, putative


Mass: 14302.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22W32

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Protein/peptide , 2 types, 4 molecules U3u3U4u4

#3: Protein/peptide Unknown peptide


Mass: 2911.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB255
#4: Protein/peptide Unknown peptide


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB255

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Cytochrome c oxidase subunit ... , 18 types, 36 molecules C1c1C2c25B5b6B6b6L6l7C7cGgIiJjKkLlOoPpRrSs...

#7: Protein Cytochrome c oxidase subunit 1


Mass: 80564.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q950Y4, cytochrome-c oxidase
#8: 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 (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
References: UniProt: Q950Y9, cytochrome-c oxidase
#10: 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 (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23FF5
#12: Protein Cytochrome c oxidase subunit 6B


Mass: 27946.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q24I72
#13: Protein Cytochrome c oxidase subunit 6B-like


Mass: 10228.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7LVX0
#16: Protein Cytochrome c oxidase subunit 7C


Mass: 28746.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7X287
#39: Protein Cytochrome c oxidase subunit TT7


Mass: 37552.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: Q23DZ5
#41: Protein Cytochrome c oxidase subunit TT9


Mass: 29865.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7LY65
#42: Protein Cytochrome c oxidase subunit TT10


Mass: 28101.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7MD70
#43: Protein Cytochrome c oxidase subunit TT11


Mass: 27034.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7X4J9
#44: Protein Cytochrome c oxidase subunit TT12


Mass: 26738.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7M3P9
#47: Protein Cytochrome c oxidase subunit TT15


Mass: 23257.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q23F08
#48: Protein Cytochrome c oxidase subunit TT16


Mass: 20007.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7M8Y9
#50: Protein Cytochrome c oxidase subunit TT18


Mass: 20025.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7MKT6
#51: Protein Cytochrome c oxidase subunit TT19


Mass: 19882.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q230X6
#54: Protein Cytochrome c oxidase subunit TT22


Mass: 17701.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7MFV5
#57: Protein Cytochrome c oxidase subunit TT25


Mass: 12273.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB210 / References: UniProt: I7M9E7
#58: Protein Cytochrome c oxidase subunit TT26


Mass: 10418.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: I7LTF1

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Cytochrome c oxidase small TIM subunit ... , 5 types, 10 molecules T2t2T3t3T4t4T5t5T6t6

#22: Protein Cytochrome c oxidase small TIM subunit 2


Mass: 8354.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: W7XDM6
#23: Protein Cytochrome c oxidase small TIM subunit 3


Mass: 10435.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q231A8
#24: Protein Cytochrome c oxidase small TIM subunit 4


Mass: 8109.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22A35
#25: Protein Cytochrome c oxidase small TIM subunit 5


Mass: 8965.917 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q22N23
#26: Protein Cytochrome c oxidase small TIM subunit 6


Mass: 8183.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
Plasmid details: Tetrahymena Stock Center at Cornell University
Strain: SB210 / References: UniProt: Q233U0

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Non-polymers , 7 types, 122 molecules

#59: Chemical
ChemComp-HEA / HEME-A


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


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#61: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#62: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#63: 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.: 68 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#64: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#65: 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

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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 / Type: COMPLEX
Details: Tetrahymena thermophila mitochondrial cytochrome c oxidase/complex IV dimer
Entity ID: #1-#58 / Source: NATURAL
Molecular weightValue: 2.7 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Cellular location: Mitochondrial inner membrane / Organelle: Mitochondria
Buffer solutionpH: 7.4
Details: Solution were made fresh from concentrated stocks, filtered and de-gassed before equilibration onto Superose6 column
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-Amino-2-(hydroxymethyl)propane-1,3-diolTris1
250 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
40.002 g/100 mlPhenylmethanesulfonyl fluoridePMSF1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: incubation time before blotting: 60s blot time: 9s blot force: 25 offset: -2 incubation after blotting: 0s

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 56818 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17478

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122+SVNrefinement
PHENIX1.19.1_4122+SVNrefinement
EM software
IDNameVersionCategory
1crYOLO1.7.6particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10cryoSPARC3.2.0initial Euler assignment
11cryoSPARC3.2.0final Euler assignment
12cryoSPARC3.2.0classification
13cryoSPARC3.2.03D reconstruction
14PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1798857
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 394262 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 34.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033195450
ELECTRON MICROSCOPYf_angle_d0.4866263900
ELECTRON MICROSCOPYf_chiral_restr0.040527330
ELECTRON MICROSCOPYf_plane_restr0.003933006
ELECTRON MICROSCOPYf_dihedral_angle_d10.850473876

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