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- PDB-6y79: Cryo-EM structure of a respiratory complex I F89A mutant -

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Entry
Database: PDB / ID: 6y79
TitleCryo-EM structure of a respiratory complex I F89A mutant
Components
  • (Acyl carrier protein ...) x 2
  • Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsOXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion proton pumping / Ubiquinone
Function / homology
Function and homology information


lipoate biosynthetic process / NADH dehydrogenase / : / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly ...lipoate biosynthetic process / NADH dehydrogenase / : / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / protein-containing complex binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit / SLBB domain / Cytochrome-c3 Hydrogenase; chain B ...NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit / SLBB domain / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Complex1_LYR-like / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / 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) / GRIM-19 / GRIM-19 protein / 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 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / 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 / Complex 1 LYR protein domain / 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:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / : / Complex 1 protein (LYR family) / 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 / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 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 / 2Fe-2S iron-sulfur cluster binding domain / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / Chem-PSC / IRON/SULFUR CLUSTER / Phosphatidylinositol / Ubiquinone-9 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / Chem-PSC / IRON/SULFUR CLUSTER / Phosphatidylinositol / Ubiquinone-9 / Chem-ZMP / Complex 1 LYR protein domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Thioredoxin-like protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / Uncharacterized protein / Zinc finger CHCC-type domain-containing protein / NAD-dependent epimerase/dehydratase domain-containing protein / NADH dehydrogenase 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase / ETC complex I subunit conserved region-domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / YALI0D10274p / YALI0E23749p / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / YALI0A17946p / YALI0F06061p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / YALI0F00924p / YALI0F17248p / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / YALI0E29095p / YALI0D00737p / YALI0F02123p / YALI0D05467p / YALI0F14003p / YALI0E28424p / YALI0E23089p / YALI0E11891p / Acyl carrier protein / YALI0D24585p / YALI0D19030p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / YALI0D04939p / YALI0C03201p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH-ubiquinone oxidoreductase / YALI0A02651p / YALI0A01419p / NUWM protein / NUVM protein / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase / Subunit NUHM of protein NADH:Ubiquinone oxidoreductase / NUGM protein / NUCM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsParey, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I.
Authors: Etienne Galemou Yoga / Kristian Parey / Amina Djurabekova / Outi Haapanen / Karin Siegmund / Klaus Zwicker / Vivek Sharma / Volker Zickermann / Heike Angerer /
Abstract: Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure ...Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure determination of this very large membrane protein complex, the coupling mechanism is a matter of ongoing debate and the function of accessory subunits surrounding the canonical core subunits is essentially unknown. Concerted rearrangements within a cluster of conserved loops of central subunits NDUFS2 (β1-β2 loop), ND1 (TMH5-6 loop) and ND3 (TMH1-2 loop) were suggested to be critical for its proton pumping mechanism. Here, we show that stabilization of the TMH1-2 loop by accessory subunit LYRM6 (NDUFA6) is pivotal for energy conversion by mitochondrial complex I. We determined the high-resolution structure of inactive mutant F89A of eukaryotic complex I from the yeast Yarrowia lipolytica and found long-range structural changes affecting the entire loop cluster. In atomistic molecular dynamics simulations of the mutant, we observed conformational transitions in the loop cluster that disrupted a putative pathway for delivery of substrate protons required in Q redox chemistry. Our results elucidate in detail the essential role of accessory subunit LYRM6 for the function of eukaryotic complex I and offer clues on its redox-linked proton pumping mechanism.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 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 / refine
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 / _pdbx_entry_details.has_protein_modification / _refine.ls_d_res_high

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Structure visualization

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Assembly

Deposited unit
A: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
B: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
C: Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
D: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
E: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
F: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
G: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
H: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
I: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
J: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
K: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
L: Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
M: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
O: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)
P: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Q: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)
R: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
S: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
U: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
X: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
Y: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
Z: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
a: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
b: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
c: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
d: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
e: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
f: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
g: Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
h: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
i: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
j: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
n: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
1: Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
2: Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
3: Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
4: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
5: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
6: Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
8: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
9: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,010,74286
Polymers978,47242
Non-polymers32,27044
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area301440 Å2
ΔGint-2025 kcal/mol
Surface area251070 Å2
MethodPISA

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Components

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Protein , 40 types, 40 molecules ABCDEFGHIJKLMPRSUWXYZabcdefghi...

#1: Protein Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 79088.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU3, UniProt: F2Z6F1*PLUS, NADH dehydrogenase
#2: Protein Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53829.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, UniProt: F2Z660*PLUS, NADH:ubiquinone reductase (H+-translocating)
#3: Protein Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 52494.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU1, UniProt: F2Z626*PLUS, NADH dehydrogenase
#4: Protein Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63, UniProt: B5FVD3*PLUS
#5: Protein Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 42765.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371BY45, UniProt: Q6C7X4*PLUS
#6: Protein Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16657.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C5F3, UniProt: Q6C4W9*PLUS
#7: Protein Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 32389.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU0, UniProt: F2Z6D7*PLUS, NADH dehydrogenase
#8: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 27247.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT9, UniProt: F2Z6C0*PLUS, NADH dehydrogenase
#9: Protein Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 25682.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT8, UniProt: F2Z619*PLUS, NADH dehydrogenase
#10: Protein Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 20849.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CB65, UniProt: Q6C674*PLUS
#11: Protein Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 23455.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#12: Protein Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I) / NADH dehydrogenase subunit 4L / subunit ND4L


Mass: 9815.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D4, NADH:ubiquinone reductase (H+-translocating)
#13: Protein Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15148.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5, UniProt: Q6C8J9*PLUS
#15: Protein Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14702.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8, UniProt: Q6CI60*PLUS
#17: Protein Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12902.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1, UniProt: Q6C9Z1*PLUS
#18: Protein Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 28479.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY23, UniProt: F2Z673*PLUS, NADH dehydrogenase
#19: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0, UniProt: Q6CGB4*PLUS
#20: Protein Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5, UniProt: B5FVF8*PLUS
#21: Protein Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4, UniProt: Q6C4A6*PLUS
#22: Protein Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18656.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0, UniProt: Q6CEK9*PLUS
#23: Protein Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19772.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3H5, UniProt: Q6CI10*PLUS
#24: Protein Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 17328.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8ND94, UniProt: Q6CA88*PLUS
#25: Protein Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8059.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#26: Protein Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 6948.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371C0F2, UniProt: B5FVE5*PLUS
#27: Protein Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11039.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596, UniProt: B5RSK3*PLUS
#28: Protein Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 7807.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NFX6
#29: Protein Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9621.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3, UniProt: Q6CD73*PLUS
#30: Protein Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8921.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0, UniProt: B5FVF3*PLUS
#31: Protein Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16175.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N5V2, UniProt: Q6CG53*PLUS
#32: Protein Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9793.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q311
#33: Protein Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10494.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY24, UniProt: B5RSK9*PLUS, NADH dehydrogenase
#34: Protein Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 13523.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A371CFV9, UniProt: Q6C1R9*PLUS
#35: Protein Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 38361.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, UniProt: Q9B6E8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#36: Protein Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53353.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, UniProt: Q9B6C8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#37: Protein Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14478.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, UniProt: Q9B6C7*PLUS, NADH:ubiquinone reductase (H+-translocating)
#38: Protein Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 54506.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TMP9, UniProt: Q9B6D6*PLUS, NADH:ubiquinone reductase (H+-translocating)
#39: Protein Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 73740.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: S5TF58, UniProt: Q9B6D3*PLUS, NADH:ubiquinone reductase (H+-translocating)
#40: Protein Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I) / NADH dehydrogenase subunit 6 / Subunit ND6


Mass: 20765.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#41: Protein Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9, UniProt: B5FVG1*PLUS
#42: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0, UniProt: B5RSL7*PLUS

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Acyl carrier protein ... , 2 types, 2 molecules OQ

#14: Protein Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS
#16: Protein Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS

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Non-polymers , 13 types, 44 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#44: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#45: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#46: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#47: 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.: 11 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#48: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#49: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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
#51: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#52: 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.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#53: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H82O4
#54: Chemical
ChemComp-T7X / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H83O13P
#55: Chemical ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE


Mass: 759.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
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: Mitochondrial NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast) / Strain: GB30
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMsodium clorideNaCl1
31 mMEDTA1
40.025 %LMNG1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 51.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2016
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 479372
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143203 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 30 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6RFR

6rfr


Accession code: 6RFR / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.96 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0167573
ELECTRON MICROSCOPYf_angle_d1.3291341
ELECTRON MICROSCOPYf_dihedral_angle_d14.05140639
ELECTRON MICROSCOPYf_chiral_restr0.06510083
ELECTRON MICROSCOPYf_plane_restr0.00911398

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