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- EMDB-10711: Cryo-EM structure of a respiratory complex I F89A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-10711
TitleCryo-EM structure of a respiratory complex I F89A mutant
Map data
SampleMitochondrial NADH:ubiquinone oxidoreductase
  • 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 NIMM 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)
  • (Acyl carrier protein ...) x 2
  • Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB6M 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 NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUNM 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 NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • (ligand) x 13
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / protein import into mitochondrial matrix / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / acyl carrier activity ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / protein import into mitochondrial matrix / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / acyl carrier activity / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / integral component of mitochondrial inner membrane / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / ubiquinone binding / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / catalytic activity / fatty acid biosynthetic process / mitochondrial intermembrane space / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / oxidation-reduction process / electron transfer activity / oxidoreductase activity / mitochondrion / membrane / integral component of membrane / metal ion binding
NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Molybdopterin oxidoreductase ...NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Molybdopterin oxidoreductase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NAD-dependent epimerase/dehydratase / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / Phosphopantetheine attachment site / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH dehydrogenase, subunit C / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH ubiquinone oxidoreductase, F subunit / CHCH / NADH:ubiquinone oxidoreductase, subunit G / NADH-quinone oxidoreductase, chain M/4 / NADH-quinone oxidoreductase, chain I / GRIM-19 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Phosphopantetheine binding ACP domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH:ubiquinone oxidoreductase, B18 subunit / Complex 1 LYR protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Ribosomal protein/NADH dehydrogenase domain / Molybdopterin oxidoreductase, 4Fe-4S domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone oxidoreductase 9.5kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NuoE domain / 2Fe-2S ferredoxin-like superfamily / [NiFe]-hydrogenase, large subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site
NUWM protein / YALI0D04939p / YALI0A01419p / YALI0A02651p / NADH-ubiquinone oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / YALI0C03201p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 ...NUWM protein / YALI0D04939p / YALI0A01419p / YALI0A02651p / NADH-ubiquinone oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / YALI0C03201p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / YALI0D19030p / Acyl carrier protein / Complex I-B14.7 / YALI0E23089p / YALI0E28424p / YALI0F14003p / YALI0D24585p / NADH-ubiquinone oxidoreductase chain 1 / NUVM protein / NUGM protein / YALI0F02123p / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NUAM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUCM protein / Subunit NUHM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NADH-ubiquinone oxidoreductase chain 3 / Subunit NUIM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / Subunit NUKM of protein NADH:Ubiquinone Oxidoreductase (Complex I) / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / YALI0D05467p / Epimerase domain-containing protein / YALI0D00737p / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Thioredoxin-like protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Acyl carrier protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GRIM-19 / Uncharacterized protein / YALI0E29095p / YALI0E28930p / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / YALI0F17248p / YALI0F00924p / YALI0F18359p / YALI0F06061p / YALI0A17946p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / YALI0E23749p / zf-CHCC domain-containing protein / YALI0D10274p / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Uncharacterized protein / Complex I-B14.7 / ETC complex I subunit conserved region-domain-containing protein / NADH-ubiquinone oxidoreductase / NADH dehydrogenase 1 beta subcomplex subunit 3 / NADH dehydrogenase subunit 2
Biological speciesYarrowia lipolytica (yeast) / Candida lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsParey K
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of a respiratory complex I F89A mutant
Authors: Parey K
Validation ReportPDB-ID: 6y79

SummaryFull reportAbout validation report
History
DepositionFeb 28, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6y79
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10711.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 334.8 Å
0.84 Å/pix.
x 400 pix.
= 334.8 Å
0.84 Å/pix.
x 400 pix.
= 334.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.06999521 - 0.13368793
Average (Standard dev.)-0.00000040657 (±0.0039716214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 334.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z334.800334.800334.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0700.134-0.000

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Supplemental data

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Sample components

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Entire Mitochondrial NADH:ubiquinone oxidoreductase

EntireName: Mitochondrial NADH:ubiquinone oxidoreductase / Number of components: 56

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Component #1: protein, Mitochondrial NADH:ubiquinone oxidoreductase

ProteinName: Mitochondrial NADH:ubiquinone oxidoreductase / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Yarrowia lipolytica (yeast) / Strain: GB30

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Component #2: protein, Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.088078 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #3: protein, Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.829508 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #4: protein, Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.494906 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #5: protein, Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.806238 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #6: protein, Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.765738 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #7: protein, Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.65792 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #8: protein, Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.389568 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #9: protein, Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.247402 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #10: protein, Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.682305 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #11: protein, Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.849551 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #12: protein, Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.455176 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #13: protein, Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.815851 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #14: protein, Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (...

ProteinName: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.14897 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #15: protein, Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreduc...

ProteinName: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.053585 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #16: protein, Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (...

ProteinName: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Details: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.702721 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #17: protein, Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreduc...

ProteinName: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.444458 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #18: protein, Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.90287 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #19: protein, Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.479941 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #20: protein, Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.355197 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #21: protein, Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.112429 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #22: protein, Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.588209 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #23: protein, Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.65608 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #24: protein, Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.772525 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #25: protein, Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.328523 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #26: protein, Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.059366 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #27: protein, Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.948902 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #28: protein, Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.039276 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #29: protein, Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.807067 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #30: protein, Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.621051 kDa
SourceSpecies: Candida lipolytica (yeast)

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Component #31: protein, Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.921152 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #32: protein, Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.175141 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #33: protein, Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.793966 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #34: protein, Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.494885 kDa
SourceSpecies: Candida lipolytica (yeast)

+
Component #35: protein, Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.523068 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #36: protein, Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.361266 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #37: protein, Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.353359 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #38: protein, Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.478329 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #39: protein, Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.506641 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #40: protein, Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.740688 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #41: protein, Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.765102 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

+
Component #42: protein, Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.219027 kDa
SourceSpecies: Candida lipolytica (yeast)

+
Component #43: protein, Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

ProteinName: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.035651 kDa
SourceSpecies: Candida lipolytica (yeast)

+
Component #44: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

+
Component #45: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

+
Component #46: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

+
Component #47: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

+
Component #48: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

+
Component #49: ligand, Lauryl Maltose Neopentyl Glycol

LigandName: Lauryl Maltose Neopentyl Glycol / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.005188 kDa

+
Component #50: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #51: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

+
Component #52: ligand, DIUNDECYL PHOSPHATIDYL CHOLINE

LigandName: DIUNDECYL PHOSPHATIDYL CHOLINE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.622834 kDa

+
Component #53: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

+
Component #54: ligand, Ubiquinone-9

LigandName: Ubiquinone-9Coenzyme Q10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.795226 kDa

+
Component #55: ligand, Phosphatidylinositol

LigandName: Phosphatidylinositol / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.887128 kDa

+
Component #56: ligand, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOY...

LigandName: (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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.759068 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 80 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 51.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500.0 - -2500.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

-
Image acquisition

Image acquisitionNumber of digital images: 2016

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 143203
3D reconstructionSoftware: RELION / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 6RFR
Overall bvalue: 30
Output model

+
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