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- PDB-6qca: Ovine respiratory complex I FRC open class 5 -

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Basic information

Entry
Database: PDB / ID: 6qca
TitleOvine respiratory complex I FRC open class 5
Components
  • (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
  • Acyl carrier protein
  • NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
  • NDUFA1
  • NDUFA11
  • NDUFA13
  • NDUFA5
  • NDUFA7
  • NDUFB1
  • NDUFB10
  • NDUFB11
  • NDUFB6
  • NDUFC1
  • NDUFS2
  • NDUFS6
  • NDUFS7
  • NDUFS8
  • NDUFV2
  • NDUFV3
KeywordsELECTRON TRANSPORT / complex I / cellular respiration / mitochondria
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / 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 / FAD binding / regulation of mitochondrial membrane potential / electron transport chain / 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 / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / metal ion binding
Similarity search - Function
Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / SLBB domain / : / FAD-binding domain / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / FAD binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit ...Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / SLBB domain / : / FAD-binding domain / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / FAD binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / 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 b14.5b (NDUFC2) / 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 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 / 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 / START-like domain superfamily / 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-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / Complex 1 LYR protein domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Complex 1 protein (LYR family) / NADH-quinone oxidoreductase, chain 5-like / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 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. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / 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 / PFC0360w protein / 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 / 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] 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 / 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 / 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 / Flavoprotein/dehydrogenase / 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: 6.2 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 27, 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 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

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Assembly

Deposited unit
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)974,49858
Polymers969,63245
Non-polymers4,86613
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 17 types, 18 molecules V1V2S2S7S8V3S6A5A7AAABAKBJAMB6BKB1A1

#1: 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)
#2: 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
#4: Protein NDUFS2


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


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


Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#8: 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
#9: Protein NDUFS6


Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Plasmid details: heart / Tissue: heart
#13: 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
#15: 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
#17: 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
#25: Protein NDUFA11


Mass: 14610.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Plasmid details: heart / Tissue: heart / References: UniProt: W5PAR2
#28: Protein NDUFB10


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


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart
#36: 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
#41: 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
#43: 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
#44: 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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NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules S1S3

#3: 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
#5: 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

#10: 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
#11: 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
#14: 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
#26: 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
#30: 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
#31: 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
#32: 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
#34: 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
#37: Protein NADH:ubiquinone oxidoreductase subunit B7


Mass: 16282.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: heart / Tissue: heart / References: UniProt: W5P5V3
#38: 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 / References: UniProt: W5PGA3
#39: 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 ... , 6 types, 6 molecules A2ALA8AJC2B8

#12: 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
#16: 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
#27: 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
#29: 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
#33: 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
#40: 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

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

#18: 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)
#19: 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)
#20: 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)
#21: 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)
#22: 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)
#23: 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)
#24: 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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Protein/peptide , 1 types, 1 molecules C1

#42: Protein/peptide NDUFC1


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 , 6 types, 13 molecules

#45: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#48: Chemical ChemComp-ZN / ZINC ION


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


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#50: 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

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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 respiratory complex I / Type: COMPLEX
Details: ovine mitochondrial respiratory complex I FRC open class 5
Entity ID: #1-#44 / Source: NATURAL
Molecular weightValue: 1.0 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: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12244 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 75 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 5LNK

5lnk


Accession code: 5LNK / Source name: PDB / Type: experimental model

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