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- PDB-7o3c: Murine supercomplex CIII2CIV in the mature unlocked conformation -

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Basic information

Entry
Database: PDB / ID: 7o3c
TitleMurine supercomplex CIII2CIV in the mature unlocked conformation
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 12
  • Cox7a2l protein
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsMEMBRANE PROTEIN / mitochondria / respiratory chain / supercomplex / OXIDOREDUCTASE / complex III / complex IV
Function / homology
Function and homology information


subthalamus development / pons development / TP53 Regulates Metabolic Genes / Respiratory electron transport / cerebellar Purkinje cell layer development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / thalamus development / Cytoprotection by HMOX1 ...subthalamus development / pons development / TP53 Regulates Metabolic Genes / Respiratory electron transport / cerebellar Purkinje cell layer development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / thalamus development / Cytoprotection by HMOX1 / respiratory chain complex IV / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / response to alkaloid / cytochrome-c oxidase / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / response to copper ion / response to glucagon / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / response to cobalamin / response to hyperoxia / ATP synthesis coupled electron transport / animal organ regeneration / enzyme regulator activity / response to cadmium ion / response to electrical stimulus / respiratory electron transport chain / lactation / cerebellum development / response to hormone / response to activity / central nervous system development / hippocampus development / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / response to toxic substance / response to calcium ion / myelin sheath / response to ethanol / mitochondrial inner membrane / response to oxidative stress / response to hypoxia / oxidoreductase activity / response to xenobiotic stimulus / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VIIa-related, mitochondrial / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV ...Cytochrome c oxidase subunit VIIa-related, mitochondrial / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / : / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / 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 oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit III-like superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / TRISTEAROYLGLYCEROL ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / TRISTEAROYLGLYCEROL / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 9 / Cox7a2l protein / Cytochrome c oxidase subunit 6C / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVercellino, I. / Sazanov, L.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission754411 Austria
CitationJournal: Nature / Year: 2021
Title: Structure and assembly of the mammalian mitochondrial supercomplex CIIICIV.
Authors: Irene Vercellino / Leonid A Sazanov /
Abstract: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is ...The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is debated. Supercomplexes CIIICIV (refs. ), CICIII (ref. ) and CICIIICIV (respirasome) exist in mammals, but in contrast to CICIII and the respirasome, to date the only known eukaryotic structures of CIIICIV come from Saccharomyces cerevisiae and plants, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIIICIV and its assembly intermediates, in different conformations. We describe the assembly of CIIICIV from the CIII precursor to the final CIIICIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. ) deep into CIII, while its C terminus is integrated into CIV. Our structures (which include CICIII and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIIICIV and has no role in the assembly of the respirasome. We show that CIII is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII, explaining the presence of one copy of CIV in CIIICIV in mammals. Finally, we show that CIII and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIIICIV in fine tuning the efficiency of electron transfer in the electron transport chain.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Oct 27, 2021Group: Data collection / Database references
Category: citation / em_admin ...citation / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code

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Structure visualization

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
L: Cytochrome b-c1 complex subunit 1, mitochondrial
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 7
R: Cytochrome b-c1 complex subunit 8
S: Cytochrome b-c1 complex subunit 6, mitochondrial
U: Cytochrome b-c1 complex subunit 9
V: Cytochrome b-c1 complex subunit 10
T: Cytochrome b-c1 complex subunit 9
I: Cox7a2l protein
a: Cytochrome c oxidase subunit 1
b: Cytochrome c oxidase subunit 2
c: Cytochrome c oxidase subunit 3
d: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
e: Cytochrome c oxidase subunit 5A, mitochondrial
f: Cytochrome c oxidase subunit 5B, mitochondrial
g: Cytochrome c oxidase subunit 6A2, mitochondrial
h: Cytochrome c oxidase subunit 6B1
i: Cytochrome c oxidase subunit 6C
k: Cytochrome c oxidase subunit 7B, mitochondrial
l: Cytochrome c oxidase subunit 7C, mitochondrial
m: Cytochrome c oxidase subunit 8B, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)716,98975
Polymers686,19434
Non-polymers30,79541
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome b-c1 complex subunit ... , 9 types, 17 molecules ALBMEPFQGRHSJUKVT

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 49355.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CZ13
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 46641.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9DB77
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21524.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CR68, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 13456.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CQB4
#7: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9652.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CQ69
#8: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 9002.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P99028
#9: Protein Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7326.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q8R1I1
#10: Protein Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 6546.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CPX8
#11: Protein Cytochrome b-c1 complex subunit 9 / Su9 / Subunit 9 / 8 kDa subunit 9 / Complex III subunit IX / Cytochrome b-c1 complex subunit 11 / ...Su9 / Subunit 9 / 8 kDa subunit 9 / Complex III subunit IX / Cytochrome b-c1 complex subunit 11 / UQCRFS1 mitochondrial targeting sequence / UQCRFS1 MTS / Ubiquinol-cytochrome c reductase 8 kDa protein


Mass: 7900.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CR68

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Protein , 3 types, 5 molecules CNDOI

#3: Protein Cytochrome b / / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 43240.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00158
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27312.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9D0M3, quinol-cytochrome-c reductase
#12: Protein Cox7a2l protein /


Mass: 12575.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q99KD6

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Cytochrome c oxidase subunit ... , 12 types, 12 molecules abcdefghiklm

#13: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I


Mass: 56945.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00397, cytochrome-c oxidase
#14: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 25993.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00405, cytochrome-c oxidase
#15: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 29948.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P00416, cytochrome-c oxidase
#16: Protein Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 17225.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P19783
#17: Protein Cytochrome c oxidase subunit 5A, mitochondrial / / Cytochrome c oxidase polypeptide Va


Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P12787
#18: Protein Cytochrome c oxidase subunit 5B, mitochondrial / / Cytochrome c oxidase polypeptide Vb


Mass: 10862.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P19536
#19: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH


Mass: 9437.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P43023
#20: Protein Cytochrome c oxidase subunit 6B1 / / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 9955.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P56391
#21: Protein Cytochrome c oxidase subunit 6C / / Cytochrome c oxidase polypeptide VIc


Mass: 8352.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: Q9CPQ1
#22: Protein Cytochrome c oxidase subunit 7B, mitochondrial / / Cytochrome c oxidase polypeptide VIIb


Mass: 6317.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P56393
#23: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / / Cytochrome c oxidase polypeptide VIIc


Mass: 5451.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P17665
#24: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H


Mass: 4660.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: heart / References: UniProt: P48772

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Non-polymers , 13 types, 41 molecules

#25: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#26: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#27: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#28: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#30: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#31: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#32: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#33: Chemical ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#35: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#36: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#37: Chemical ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H110O6

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Details

Has ligand of interestN

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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: Murine full supercomplex CIII2CIV in the unlocked conformation
Type: COMPLEX
Details: Dimer of Complex III, monomer of complex IV, bridged by SCAF1
Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 0.7 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Cellular location: inner mitochondrial membrane / Organ: heart / Organelle: mitochondria / Tissue: cardiac muscle
Buffer solutionpH: 7.7 / Details: CHAPS was added only upon freezing
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaClSodium chloride1
32 mMEDTAEthylenediaminetetraacetic acidC10H16N2O81
40.2 %CHAPSC32H58N2O7S1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.17 sec. / Electron dose: 90.66 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7245

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
EM software
IDNameVersionCategoryDetails
1EPUimage acquisition
12Cootmodel fitting
20RELION3.1particle selection
21Topazparticle selection
23GctfCTF correctionused for per-particle defocus
24CTFFINDCTF correctionused for initial CTF estimation
25RELION3.1CTF correctionused for CTF refinement
27RELION3.1initial Euler assignment
29RELION3.1final Euler assignment
31RELION3.1classification
33RELION3.13D reconstruction
34PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1500000
Details: multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16228 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 80 / Protocol: OTHER / Space: REAL / Target criteria: MAXIMAL LIKELYHOOD
Atomic model building
IDPDB-ID 3D fitting-ID
11NTZ

1ntz

1
23L75

3l75

1
35IY5

5iy5

1
45Z62

5z62

1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 80.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005949804
ELECTRON MICROSCOPYf_angle_d1.057967589
ELECTRON MICROSCOPYf_chiral_restr0.06067278
ELECTRON MICROSCOPYf_plane_restr0.0088480
ELECTRON MICROSCOPYf_dihedral_angle_d7.98447385

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