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- PDB-6qc4: Ovine respiratory supercomplex I+III2 open class 3 -

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Basic information

Entry
Database: PDB / ID: 6qc4
TitleOvine respiratory supercomplex I+III2 open class 3
Components
  • (Cytochrome b-c1 complex subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 2
  • (NADH:ubiquinone oxidoreductase subunit ...) x 11
  • (Ubiquinol-cytochrome c reductase ...) x 2
  • Acyl carrier protein
  • Cytochrome b
  • Cytochrome c1
  • NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
  • NDUFA11
  • NDUFA13
  • NDUFA1NADH dehydrogenase (ubiquinone), alpha 1
  • NDUFA5
  • NDUFA7
  • NDUFB10
  • NDUFB11
  • NDUFB1
  • NDUFB6
  • NDUFC1
  • NDUFS2
  • NDUFS6
  • NDUFS7
  • NDUFS8
  • NDUFV2
  • NDUFV3
  • UQCRB
  • UQCRC1
  • UQCRFS1N
  • Ubiquinol-cytochrome c reductase, complex III subunit X
KeywordsELECTRON TRANSPORT / supercomplex / cellular respiration / mitochondria
Function / homology
Function and homology information


subthalamus development / pons development / respiratory chain complex III / cerebellar Purkinje cell layer development / pyramidal neuron development / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / blastocyst hatching / thalamus development / NADH dehydrogenase activity ...subthalamus development / pons development / respiratory chain complex III / cerebellar Purkinje cell layer development / pyramidal neuron development / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / blastocyst hatching / thalamus development / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex IV / ubiquinol-cytochrome-c reductase activity / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial large ribosomal subunit / midbrain development / electron transport chain / hypothalamus development / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respirasome / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / hippocampus development / 2 iron, 2 sulfur cluster binding / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / brain development / mitochondrial inner membrane / response to oxidative stress / nuclear body / electron transfer activity / mitochondrial matrix / oxidoreductase activity / proteolysis / protein-containing complex binding / heme binding / integral component of membrane / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Tim17/Tim22/Tim23/Pmp24 family / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / 2Fe-2S iron-sulfur cluster binding domain / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) ...Tim17/Tim22/Tim23/Pmp24 family / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / 2Fe-2S iron-sulfur cluster binding domain / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / Globular protein, non-globular alpha/beta subunit / Thioredoxin-like [2Fe-2S] ferredoxin / Cytochrome b-c1 complex, subunit 6 / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2 C-terminus / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / Cytochrome b-c1 complex subunit 8 / UcrQ family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit 8 superfamily / Ubiquinol cytochrome reductase transmembrane region / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / Cytochrome c1, transmembrane anchor, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Cytochrome b / Cytochrome c1 / Cytochrome C1 family / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6/petB / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH:ubiquinone oxidoreductase, subunit G / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Deoxynucleoside kinase / Deoxynucleoside kinase domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Cytochrome b/b6 N-terminal region profile.
Similarity search - Domain/homology
Complex I-MNLL / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-B22 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / Complex III subunit 8 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-AGGG ...Complex I-MNLL / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-B22 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / Complex III subunit 8 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-AGGG / Complex I-ESSS / Cytochrome b-c1 complex subunit 2, mitochondrial / Complex I-B17 / Cytochrome c1, heme protein, mitochondrial / Complex I-15 kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-B14 / Complex I-B15 / Complex I-B14.7 / FE2/S2 (INORGANIC) CLUSTER / Complex III subunit 9 / NADH-ubiquinone oxidoreductase chain 2 / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Chem-ZMP / FLAVIN MONONUCLEOTIDE / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Cytochrome b-c1 complex subunit 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 3 / Complex I-B18 / 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 / Complex I-B9 / Complex I-B14.5a / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex I-SGDH
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 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]

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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: UQCRFS1N
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: UQCRFS1N
i2: Ubiquinol-cytochrome c reductase, complex III subunit X
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: NDUFA11
B5: NADH:ubiquinone oxidoreductase subunit B5
AB: Acyl carrier protein
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
BJ: NDUFB10
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: NDUFA13
B6: NDUFB6
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: NDUFB11
C1: NDUFC1
B1: NDUFB1
A1: NDUFA1
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NDUFV2
S1: NADH:ubiquinone oxidoreductase core subunit S1
S2: NDUFS2
S3: NADH:ubiquinone oxidoreductase core subunit S3
S7: NDUFS7
S8: NDUFS8
V3: NDUFV3
S6: NDUFS6
S4: NADH:ubiquinone oxidoreductase subunit S4
A9: NADH:ubiquinone oxidoreductase subunit A9
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A5: NDUFA5
A6: NADH:ubiquinone oxidoreductase subunit A6
A7: NDUFA7
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AA: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,445,95387
Polymers1,436,24265
Non-polymers9,71122
Water0
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 , 23 types, 30 molecules a1a3b1b2c1c2d1d2x1x2i1i2AKABAABJAMB6BKB1A1V1V2S2S7S8V3S6A5A7

#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
#9: Protein UQCRFS1N / UQCRFS1N


Mass: 6656.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#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
#18: Protein NDUFA11 /


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
#20: 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
#22: Protein NDUFB10 / / NDUFV2


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#29: Protein NDUFA13 / / MT-ND3


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#30: Protein NDUFB6 /


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
#35: Protein NDUFB11 /


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
#37: Protein NDUFB1 /


Mass: 6930.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5QG39
#38: Protein NDUFA1 / NADH dehydrogenase (ubiquinone), alpha 1


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#39: 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)
#40: Protein NDUFV2 /


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
#42: Protein NDUFS2 / / MT-ND4


Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#44: Protein NDUFS7 / / NDUFA11


Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#45: Protein NDUFS8 / / NDUFB5


Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#46: Protein NDUFV3 / / NDUFA8


Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#47: Protein NDUFS6 / / NDUFAB1


Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#51: Protein NDUFA5 /


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
#53: Protein NDUFA7 /


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

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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 ... , 2 types, 4 molecules f1f2h1h2

#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
#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

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

#11: 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)
#12: 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)
#13: 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)
#14: 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)
#15: 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)
#16: 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)
#17: 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:ubiquinone oxidoreductase subunit ... , 11 types, 11 molecules B5S5A3B3B4B7B9B2S4A9A6

#19: 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
#24: 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
#25: 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
#26: 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
#28: 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
#31: 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
#32: 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
#33: 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
#48: 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
#49: 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
#52: 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

+
NADH dehydrogenase [ubiquinone] 1 ... , 6 types, 6 molecules A8AJC2B8A2AL

#21: 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
#23: 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
#27: 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
#34: 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
#50: 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
#54: 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

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Protein/peptide , 1 types, 1 molecules C1

#36: Protein/peptide NDUFC1 / / NDUFA7


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

#41: 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
#43: 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) / Plasmid details: heart / Tissue: heart / References: UniProt: W5PB27

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Non-polymers , 9 types, 22 molecules

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


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


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


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#58: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#59: 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
#60: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


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


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


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ovine mitochondrial respiratory supercomplex I+III2 / Type: COMPLEX
Details: Open class 3 from ovine mitochondrial 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 chlorideNaClSodium chloride1
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 FIELDBright-field microscopy / Calibrated magnification: 100000 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm
Specimen holderCryogen: NITROGEN / 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
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.13-2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 400000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14230 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
11PPJ1
25LNK1

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