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- PDB-7b0n: A 3.7-angstrom structure of Yarrowia lipolytica complex I with an... -

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Basic information

Entry
Database: PDB / ID: 7b0n
TitleA 3.7-angstrom structure of Yarrowia lipolytica complex I with an R121M mutation in NUCM.
Components
  • (Acyl carrier ...) x 2
  • (NADH dehydrogenase ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • Complex I-B14.7
  • Epimerase domain-containing protein
  • GRIM-19
  • NUCM protein
  • NUGM protein
  • 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 NB8M 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 NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM 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)
  • subunit NEBM of protein NADH:Ubiquinone Oxidoreductase (Complex I) [Yarrowia lipolytica]
  • subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • zf-CHCC domain-containing protein
KeywordsMEMBRANE PROTEIN / NADH:Ubiquinone Oxidoreductase / complex I
Function / homology
Function and homology information


NADH dehydrogenase / respiratory chain complex I / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / : / ubiquinone binding ...NADH dehydrogenase / respiratory chain complex I / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / electron transport chain / 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 / 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 / Soluble ligand binding domain / SLBB domain / NADH-ubiquinone oxidoreductase, subunit 10 / 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 / Soluble ligand binding domain / SLBB domain / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / 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 / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / 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 / NDUFB9, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / 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/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Complex 1 LYR protein domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / 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 / Complex 1 protein (LYR family) / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / 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 / NADH dehydrogenase / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / CHCH / CHCH domain / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NuoE domain / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Complex 1 LYR protein domain-containing protein / Uncharacterized protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / 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 / Uncharacterized protein / 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 / NUWM protein / NUVM protein / 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 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHirst, J. / Grba, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105663141 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: J Biol Chem / Year: 2021
Title: A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I.
Authors: Mikhail A Hameedi / Daniel N Grba / Katherine H Richardson / Andrew J Y Jones / Wei Song / Maxie M Roessler / John J Wright / Judy Hirst /
Abstract: Respiratory complex I (NADH:ubiquinone oxidoreductase), the first enzyme of the electron-transport chain, captures the free energy released by NADH oxidation and ubiquinone reduction to translocate ...Respiratory complex I (NADH:ubiquinone oxidoreductase), the first enzyme of the electron-transport chain, captures the free energy released by NADH oxidation and ubiquinone reduction to translocate protons across an energy-transducing membrane and drive ATP synthesis during oxidative phosphorylation. The cofactor that transfers the electrons directly to ubiquinone is an iron-sulfur cluster (N2) located in the NDUFS2/NUCM subunit. A nearby arginine residue (R121), which forms part of the second coordination sphere of the N2 cluster, is known to be posttranslationally dimethylated but its functional and structural significance are not known. Here, we show that mutations of this arginine residue (R121M/K) abolish the quinone-reductase activity, concomitant with disappearance of the N2 signature from the electron paramagnetic resonance (EPR) spectrum. Analysis of the cryo-EM structure of NDUFS2-R121M complex I at 3.7 Å resolution identified the absence of the cubane N2 cluster as the cause of the dysfunction, within an otherwise intact enzyme. The mutation further induced localized disorder in nearby elements of the quinone-binding site, consistent with the close connections between the cluster and substrate-binding regions. Our results demonstrate that R121 is required for the formation and/or stability of the N2 cluster and highlight the importance of structural analyses for mechanistic interpretation of biochemical and spectroscopic data on complex I variants.
History
DepositionNov 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 2, 2021Group: Atomic model / Category: atom_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jul 21, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_volume / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / em_entity_assembly / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_entity_assembly.entity_id_list / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
B: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
C: NUGM protein
D: NUCM protein
E: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
F: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
G: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
H: NADH-ubiquinone oxidoreductase chain 1
I: Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH dehydrogenase subunit 2
O: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
P: Epimerase domain-containing protein
Q: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
R: zf-CHCC domain-containing protein
S: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
T: Acyl carrier protein
U: Acyl carrier protein
V: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
X: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
Y: Complex I-B14.7
Z: GRIM-19
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
c: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
d: subunit NEBM of protein NADH:Ubiquinone Oxidoreductase (Complex I) [Yarrowia lipolytica]
e: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
f: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
g: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
h: subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
i: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
j: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
k: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
l: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
m: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
n: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
o: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
p: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)990,18780
Polymers963,83742
Non-polymers26,35038
Water00
1


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

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Components

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NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJKLM

#1: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 14506.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad3, YALI1_M00472r / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 38389.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (PLC)(3PE)(3PE) are not in the polypeptide sequence (FME) is at the start of the polypeptide sequence
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad1, YALI1_M00064g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 20793.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (FME) is in the polypeptide sequence / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad6, YALI1_M00056g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U3X7, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 4L


Mass: 9843.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (FME) is in the polypeptide sequence / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4L, YALI1_M00335g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U4U1, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 73768.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (PLC)(3PE)(3PE)(3PE)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad5, YALI1_M00338r / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TF58, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 54534.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (CDL)(PLC)(PLC)(3PE)(LMT)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4, YALI1_M00296g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TMP9, NADH:ubiquinone reductase (H+-translocating)

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Protein , 32 types, 32 molecules BCDEFGIOPQRSVWXYZbcdefghijklmnop

#2: Protein Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 23455.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nukm, YALI1_F09003g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#3: Protein NUGM protein


Mass: 33644.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nugm, B0I71DRAFT_126141 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU0, NADH dehydrogenase
#4: Protein NUCM protein


Mass: 52468.906 Da / Num. of mol.: 1 / Mutation: R121M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nucm, B0I71DRAFT_131656, YALI1_F22993g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU1, NADH dehydrogenase
#5: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 27247.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuhm / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT9, NADH dehydrogenase
#6: Protein Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53829.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nubm, NUO51, YALI1_B26679g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, NADH:ubiquinone reductase (H+-translocating)
#7: Protein Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 79088.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuam, YALI1_D07089g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU3, NADH dehydrogenase
#9: Protein Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase


Mass: 21890.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ligands (SF4)(SF4) are not in the polypeptide sequence
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuim, B0I71DRAFT_132693, YALI1_F01456g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT8, NADH dehydrogenase
#15: Protein Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18588.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (CDL) is not in the polypeptide sequence / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E33570g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4
#16: Protein Epimerase domain-containing protein


Mass: 40488.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (NDP) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_137087 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371BY45
#17: Protein Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18656.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_B19507g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0
#18: Protein zf-CHCC domain-containing protein


Mass: 13133.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (ZN) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_130567, YALI1_D24109g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5
#19: Protein Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9621.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_C04281g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3
#22: Protein Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16657.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_119420, BD777DRAFT_112063 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C5F3
#23: Protein Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14778.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_A01824g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8
#24: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_134276 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0
#25: Protein Complex I-B14.7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase subunit B14.7


Mass: 18966.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (LMT) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129038 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371CB65
#26: Protein GRIM-19


Mass: 13981.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (CDL)(3PE) are not in the polypeptide chain
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_132113, YALI1_E34222g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5
#28: Protein subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8992.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (CDL)(3PE)(3PE) are not in the polypeptide chain
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_131413, YALI1_E28107g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0
#29: Protein Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19772.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129288, YALI1_A03153g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3H5
#30: Protein subunit NEBM of protein NADH:Ubiquinone Oxidoreductase (Complex I) [Yarrowia lipolytica]


Mass: 7928.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E00527g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#31: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_F24343g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0
#32: Protein Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16175.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_100046, YALI1_B00908g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N5V2
#33: Protein Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 28479.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuwm, B0I71DRAFT_98177, YALI1_E34367g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q6ZY23, NADH dehydrogenase
#34: Protein subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15818.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_126580 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371CFV9
#35: Protein Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9793.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_133979, YALI1_D22691g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q311
#36: Protein Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 7807.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129560, YALI1_D30003g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NFX6
#37: Protein Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 6948.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_135324 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C0F2
#38: Protein Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 17328.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129122, YALI1_D06302g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8ND94
#39: Protein Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10494.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuvm, YALI1_F09017g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q6ZY24, NADH dehydrogenase
#40: Protein Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12902.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D09203g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1
#41: Protein Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11219.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E37603g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9
#42: Protein Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11039.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_A18188g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596

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NADH dehydrogenase ... , 2 types, 2 molecules Na

#14: Protein NADH dehydrogenase subunit 2


Mass: 53381.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligands (PLC)(PLC)(3PE) are not in the polypeptide sequence (FME) is in the polypeptide sequence
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad2, YALI1_M00458g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, NADH:ubiquinone reductase (H+-translocating)
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 9675.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ligand (CDL) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_173710, YALI1_C30086g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63

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Acyl carrier ... , 2 types, 2 molecules TU

#20: Protein Acyl carrier protein


Mass: 8821.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (EHZ) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_165126, YALI1_D18037g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9
#21: Protein Acyl carrier protein


Mass: 9533.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (EHZ) is not in the polypeptide chain / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D32594g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21

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Sugars , 1 types, 2 molecules

#52: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 36 molecules

#43: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#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.: 13 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#48: 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
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#51: Chemical ChemComp-EHZ / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate


Mass: 584.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O9PS

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxidoreductase) with NUCM R121M mutation
Type: COMPLEX
Entity ID: #1, #10-#11, #15-#19, #2, #20-#29, #3, #30-#39, #4, #40-#42, #5-#9
Source: RECOMBINANT
Source (natural)Organism: Yarrowia lipolytica (yeast)
Source (recombinant)Organism: Yarrowia lipolytica (yeast) / Strain: GB10
Buffer solutionpH: 7.45
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PEG-thiol treated / Grid material: GOLD / Grid type: UltrAuFoil
VitrificationCryogen name: ETHANE

-
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: 130000 X / Calibrated defocus min: -1500 nm / Calibrated defocus max: -2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2241
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4RELION3.1CTF correction
5GctfCTF correction
8UCSF Chimera1.13.1model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 110787 / Details: Post manual curation of Relion auto-pick
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21013 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6YJ4

6yj4

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