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- PDB-6qc3: Ovine respiratory supercomplex I+III2 open class 1 -

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Basic information

Entry
Database: PDB / ID: 6qc3
TitleOvine respiratory supercomplex I+III2 open class 1
Components
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 7
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 3
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 2
  • (NADH:ubiquinone oxidoreductase subunit ...) x 11
  • (NDUFA1) x 2
  • (Ubiquinol-cytochrome c reductase ...) x 2
  • Acyl carrier protein
  • Cytochrome b
  • Cytochrome b-c1 complex subunit 6
  • Cytochrome c1
  • MT-ND1
  • MT-ND5
  • NADH dehydrogenase [ubiquinone] 1 subunit C2
  • NDUFA13
  • NDUFB1
  • NDUFB11
  • NDUFB4
  • NDUFB6
  • NDUFV3
  • UQCRB
  • UQCRC1
  • Ubiquinol-cytochrome c reductase, complex III subunit X
KeywordsELECTRON TRANSPORT / supercomplex / cellular respiration / mitochondria
Function / homology
Function and homology information


: / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly ...: / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / respiratory chain complex I / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / membrane => GO:0016020 / : / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / electron transport chain / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / heme binding / protein-containing complex binding / proteolysis / nucleoplasm / metal ion binding
Similarity search - Function
SLBB domain / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily ...SLBB domain / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome b-c1 complex, subunit 6 / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 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 b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / 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 b / : / 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. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Tim17/Tim22/Tim23/Pmp24 family / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / : / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Metalloenzyme, LuxS/M16 peptidase-like / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / SLBB domain / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Cytochrome b-c1 complex subunit 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome b / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex III subunit 9 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Cytochrome b-c1 complex subunit 8 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLetts, J.A. / Sazanov, L.A.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Jun 2, 2021Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

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Assembly

Deposited unit
a1: UQCRC1
a2: Ubiquinol-cytochrome c reductase core protein 2
b1: Cytochrome b
c1: Cytochrome c1
f1: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d1: UQCRB
q1: Ubiquinol-cytochrome c reductase complex III subunit VII
h1: Cytochrome b-c1 complex subunit 6
x1: Cytochrome b-c1 complex subunit Rieske, mitochondrial
i1: Ubiquinol-cytochrome c reductase, complex III subunit X
a3: UQCRC1
a4: Ubiquinol-cytochrome c reductase core protein 2
b2: Cytochrome b
c2: Cytochrome c1
f2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d2: UQCRB
q2: Ubiquinol-cytochrome c reductase complex III subunit VII
h2: Cytochrome b-c1 complex subunit 6
x2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
i2: Ubiquinol-cytochrome c reductase, complex III subunit X
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
S1: NADH:ubiquinone oxidoreductase core subunit S1
S2: NDUFB11
S3: NADH:ubiquinone oxidoreductase core subunit S3
S7: NDUFB1
S8: NDUFA1
V3: NDUFV3
S6: NDUFB6
S4: NADH:ubiquinone oxidoreductase subunit S4
A9: NADH:ubiquinone oxidoreductase subunit A9
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
A6: NADH:ubiquinone oxidoreductase subunit A6
A7: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AA: Acyl carrier protein
D3: NADH-ubiquinone oxidoreductase chain 3
D1: NADH-ubiquinone oxidoreductase chain 1
D6: NADH-ubiquinone oxidoreductase chain 6
4L: NADH-ubiquinone oxidoreductase chain 4L
D5: NADH-ubiquinone oxidoreductase chain 5
D4: NADH-ubiquinone oxidoreductase chain 4
D2: NADH-ubiquinone oxidoreductase chain 2
AK: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
B5: NADH:ubiquinone oxidoreductase subunit B5
AB: Acyl carrier protein
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
BJ: MT-ND5
AJ: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
S5: NADH:ubiquinone oxidoreductase subunit S5
A3: NADH:ubiquinone oxidoreductase subunit A3
B3: NADH:ubiquinone oxidoreductase subunit B3
C2: NADH dehydrogenase [ubiquinone] 1 subunit C2
B4: NADH:ubiquinone oxidoreductase subunit B4
AM: MT-ND1
B6: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
B7: NADH:ubiquinone oxidoreductase subunit B7
B9: NADH:ubiquinone oxidoreductase subunit B9
B2: NADH:ubiquinone oxidoreductase subunit B2
B8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
BK: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
C1: NDUFB4
B1: NDUFA13
A1: NDUFA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,442,30793
Polymers1,427,39265
Non-polymers14,91528
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 17 types, 24 molecules a1a3b1b2c1c2d1d2h1h2i1i2S2S7S8V3S6AAABBJC2AMB1A1

#1: Protein UQCRC1 / UQCRC1


Mass: 49385.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart / Tissue: Heart
#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: 42877.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: P24959
#4: Protein Cytochrome c1


Mass: 27322.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5Q0A9
#6: Protein UQCRB / UQCRB


Mass: 13432.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#8: Protein Cytochrome b-c1 complex subunit 6


Mass: 9223.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: B9VH04
#10: Protein Ubiquinol-cytochrome c reductase, complex III subunit X


Mass: 7310.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P6B2
#14: Protein NDUFB11 / NDUFB11


Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#16: Protein NDUFB1 / NDUFB1


Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#17: Protein NDUFA1 / NDUFA1


Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#18: Protein NDUFV3


Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#19: Protein NDUFB6 / NDUFB6


Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#27: Protein Acyl carrier protein


Mass: 10119.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5NQT7
#38: Protein MT-ND5 / MT-ND4


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#43: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P9Q8
#45: Protein MT-ND1 / MT-ND6


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#53: Protein NDUFA13 / MT-ND3


Mass: 6930.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#54: Protein NDUFA1


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart

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Ubiquinol-cytochrome c reductase ... , 2 types, 4 molecules a2a4q1q2

#2: Protein Ubiquinol-cytochrome c reductase core protein 2


Mass: 46655.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart / Tissue: Heart / References: UniProt: W5Q0F9
#7: Protein Ubiquinol-cytochrome c reductase complex III subunit VII


Mass: 9606.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PUP9

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Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules f1f2x1x2

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 21654.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P2X9, quinol-cytochrome-c reductase
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / UQCRFS1N


Mass: 2230.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: modeled as poly-UNK due to disorder / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2

#11: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 48678.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NDUFB2


Mass: 23840.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5NRY1

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NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules S1S3

#13: Protein NADH:ubiquinone oxidoreductase core subunit S1


Mass: 77031.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QB34
#15: Protein NADH:ubiquinone oxidoreductase core subunit S3


Mass: 26441.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PB27

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NADH:ubiquinone oxidoreductase subunit ... , 11 types, 11 molecules S4A9A6B5S5A3B3B4B7B9B2

#20: Protein NADH:ubiquinone oxidoreductase subunit S4


Mass: 15375.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PE07
#21: Protein NADH:ubiquinone oxidoreductase subunit A9


Mass: 38660.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PI58
#24: Protein NADH:ubiquinone oxidoreductase subunit A6


Mass: 14923.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QC06
#36: Protein NADH:ubiquinone oxidoreductase subunit B5


Mass: 16714.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QHN8
#40: Protein NADH:ubiquinone oxidoreductase subunit S5


Mass: 12474.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QFF9
#41: Protein NADH:ubiquinone oxidoreductase subunit A3


Mass: 9194.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5NYM7
#42: Protein NADH:ubiquinone oxidoreductase subunit B3


Mass: 11015.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5Q5T4
#44: Protein NADH:ubiquinone oxidoreductase subunit B4


Mass: 14975.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QF73
#47: Protein NADH:ubiquinone oxidoreductase subunit B7


Mass: 14645.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P5V3
#48: Protein NADH:ubiquinone oxidoreductase subunit B9


Mass: 21648.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PGA3
#49: Protein NADH:ubiquinone oxidoreductase subunit B2


Mass: 8500.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PVD7

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 7 types, 7 molecules A2A5A7ALAKA8AJ

#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QAH8
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NDUFS3


Mass: 13156.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PNX7
#25: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NDUFS8


Mass: 12399.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P0I2
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: B9VGZ9
#35: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14610.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PAR2
#37: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20008.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PYA5
#39: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 36803.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QBF5

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules D3D1D64LD5D4D2

#28: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating)
#29: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating)
#30: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating)
#31: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10840.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating)
#32: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68410.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating)
#33: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 52058.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating)
#34: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 3 types, 3 molecules B6B8BK

#46: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6


Mass: 15433.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PZE3
#50: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18818.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5Q1B0
#51: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NDUFC2


Mass: 14455.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5PWF1

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Protein/peptide , 1 types, 1 molecules C1

#52: Protein/peptide NDUFB4 / NDUFA13


Mass: 5808.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart

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Non-polymers , 11 types, 28 molecules

#55: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#57: 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.: 5 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#58: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#59: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#60: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#62: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#63: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#64: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#65: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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Details

Has protein modificationY

-
Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Ovine mitochondrial respiratory supercomplex I+III2 / Type: COMPLEX / Details: Open class 1 from ovine respiratory SC I+III2 / Entity ID: #1-#54 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep) / Cellular location: Mitochondrial inner membrane / Organ: Heart / Organelle: Mitochondria / Tissue: Cardiac
Buffer solutionpH: 7.4 / Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
Buffer component
IDConc.NameFormulaBuffer-ID
10.25 Msodium chlorideNaCl1
20.02 MHEPES1
30.02 %Brij-351
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 95 % / Chamber temperature: 277 K
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing

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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: OTHER
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 100000 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1854
Image scansMovie frames/image: 34

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9PHENIX1.13-2998model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 400000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35640 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 1PPJ

1ppj


Accession code: 1PPJ / Source name: PDB / Type: experimental model

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