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- PDB-6q9b: CI Membrane Arm focused refinement from Ovine respiratory SC I+III2 -

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Basic information

Entry
Database: PDB / ID: 6q9b
TitleCI Membrane Arm focused refinement from Ovine respiratory SC I+III2
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 5
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 4
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 9
  • Acyl carrier protein
  • NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
KeywordsELECTRON TRANSPORT / complex I / membrane arm / cellular respiration / mitochondria
Function / homology
Function and homology information


: / : / oxidoreductase activity, acting on NAD(P)H / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone ...: / : / oxidoreductase activity, acting on NAD(P)H / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / membrane => GO:0016020 / quinone binding / ATP synthesis coupled electron transport / reactive oxygen species metabolic process / electron transport chain / mitochondrial intermembrane space / NAD binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / mitochondrial matrix / mitochondrion
Similarity search - Function
NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / 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, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / 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 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / 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 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / [NiFe]-hydrogenase, large subunit / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / 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 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / 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 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, 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 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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 17, 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 1.4Nov 20, 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
S2: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
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: NADH:ubiquinone oxidoreductase subunit B10
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: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
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: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
B1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
A1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)614,01842
Polymers601,52429
Non-polymers12,49413
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules S2AB

#1: Protein NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2


Mass: 49193.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Since this is a focused refinement only the N-terminal part of this subunit is present in the density.,Since this is a focused refinement only the N-terminal part of this subunit is present in the density.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PJ73
#11: Protein Acyl carrier protein


Mass: 10119.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The first residue is disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5NQT7

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

#2: 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
Details: There is a disordered region in the protein that is not modeled.
Source: (natural) Ovis aries (sheep)
References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating)
#3: 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
Details: There is a disordered region in the protein that is not modeled.
Source: (natural) Ovis aries (sheep)
References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating)
#4: 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
Details: There is a disordered region in the protein that was not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating)
#5: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating)
#6: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating)
#7: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating)
#8: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 5 types, 5 molecules AKA8AJAMA1

#9: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PAR2
#12: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PYA5
#14: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5QBF5
#20: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Because this is a focused refinement only the C-terminal part of this subunit is present in the density.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
#29: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac

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NADH:ubiquinone oxidoreductase subunit ... , 9 types, 9 molecules B5BJS5A3B3B4B7B9B2

#10: Protein NADH:ubiquinone oxidoreductase subunit B5


Mass: 16714.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: First few residues are disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5QHN8
#13: Protein NADH:ubiquinone oxidoreductase subunit B10


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Some residues are disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac
#15: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5QFF9
#16: Protein NADH:ubiquinone oxidoreductase subunit A3


Mass: 9194.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N-terminus is disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5NYM7
#17: Protein NADH:ubiquinone oxidoreductase subunit B3


Mass: 11015.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The termini are disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5Q5T4
#19: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5QF73
#22: Protein NADH:ubiquinone oxidoreductase subunit B7


Mass: 16282.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The C-terminus of this subunit was disordered and therefore not modeled
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5P5V3
#23: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PGA3
#24: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PVD7

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules C2C1

#18: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N-terminal residue is disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5P9Q8
#27: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 5808.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 4 types, 4 molecules B6B8BKB1

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


Mass: 15433.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Disordered regions of this subunit were not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PZE3
#25: 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
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5Q1B0
#26: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 14455.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N-terminus was disordered and therefore not modeled.
Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5PWF1
#28: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1


Mass: 6930.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Heart
Plasmid details: Ovis aries (sheep) hearts were purchased from C Humphreys & Sons (Chelmsford, UK).
Tissue: Cardiac / References: UniProt: W5QG39

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Non-polymers , 4 types, 13 molecules

#30: 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.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#31: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#32: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#33: 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.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS

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Details

Has protein modificationY

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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: Ovine mitochondrial SC I+III2 / Type: COMPLEX
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Entity ID: #1-#29 / 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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
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
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
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174334 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 1LNK

1lnk


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

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