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- PDB-6rfs: Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4 -

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Entry
Database: PDB / ID: 6rfs
TitleCryo-EM structure of a respiratory complex I mutant lacking NDUFS4
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 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 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 / membrane protein complex / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / membrane protein complex / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly / acyl binding / ubiquinone binding / electron transport coupled proton transport / protein import into mitochondrial matrix / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / catalytic complex / 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 / metal ion binding / membrane
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 / SLBB domain / Complex1_LYR-like / NADH-ubiquinone oxidoreductase, subunit 10 ...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 / SLBB domain / Complex1_LYR-like / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / 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 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / 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-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / : / 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, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 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 / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / Complex 1 LYR protein domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / Complex 1 LYR protein domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / 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 / YALI0A17946p / YALI0F06061p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / YALI0F00924p / YALI0F17248p / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / YALI0E29095p / YALI0D00737p / YALI0F02123p / YALI0D05467p / YALI0F14003p / YALI0F06050p / YALI0E28424p / YALI0E23089p / YALI0E11891p / Acyl carrier protein / YALI0D24585p / YALI0D19030p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / YALI0D04939p / YALI0C03201p / 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: 4.04 Å
AuthorsParey, K. / Vonck, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationZI 552/4-2 Germany
CitationJournal: Sci Adv / Year: 2019
Title: High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.
Authors: Kristian Parey / Outi Haapanen / Vivek Sharma / Harald Köfeler / Thomas Züllig / Simone Prinz / Karin Siegmund / Ilka Wittig / Deryck J Mills / Janet Vonck / Werner Kühlbrandt / Volker Zickermann /
Abstract: Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is ...Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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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 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)
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)964,18953
Polymers959,89241
Non-polymers4,29712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, subunits built into 4 ? cryo-EM map
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area232280 Å2
ΔGint-1562 kcal/mol
Surface area265230 Å2
MethodPISA

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Components

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Protein , 39 types, 39 molecules ABCDEFGHIJKLMPRSUWXZabcdefghij...

#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 dehydrogenase, 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, UniProt: Q6C2Q1*PLUS, 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 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)


Mass: 14778.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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)
#35: 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)
#36: 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)
#37: 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)
#38: 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)
#39: 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)
#40: 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
#41: 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 , 6 types, 12 molecules

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


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


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


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


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#46: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#47: 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: Mitochondrial NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#41 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMSodium ChlorideNaCl1
31 mMEDTA1
40.025 %DDM1
SpecimenConc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 200000 X / Calibrated magnification: 45872 X / Nominal defocus max: -3000 nm / Nominal defocus min: -2000 nm / Cs: 2 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5964
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2Leginon1image acquisition
4GctfCTF correction
7Coot0.8.8.model fitting
9PHENIX1.12_2829model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 418740
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145767 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementHighest resolution: 4.04 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01362569
ELECTRON MICROSCOPYf_angle_d1.22284896
ELECTRON MICROSCOPYf_dihedral_angle_d13.11837161
ELECTRON MICROSCOPYf_chiral_restr0.0629489
ELECTRON MICROSCOPYf_plane_restr0.00810791

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