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- EMDB-11251: Complex I with NADH, open3 -

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Basic information

Entry
Database: EMDB / ID: EMD-11251
TitleComplex I with NADH, open3
Map data
SampleComplex I with NADH, open3
  • (NADH dehydrogenase [ubiquinone] ...) x 8
  • (Mitochondrial complex I, ...Respiratory complex I) x 16
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 10
  • Acyl carrier protein
  • (ligand) x 14
Function / homology
Function and homology information


blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / electron transport chain / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respirasome / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / brain development / mitochondrial inner membrane / response to oxidative stress / nuclear body / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / integral component of membrane / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 ...NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2 C-terminus / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / 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 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH ubiquinone oxidoreductase, F 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 oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Deoxynucleoside kinase / Deoxynucleoside kinase domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH dehydrogenase, subunit C / Soluble ligand binding domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / SLBB domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter
Similarity search - Domain/homology
Complex I-B22 / Complex I-B17 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-AGGG / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-15 kDa ...Complex I-B22 / Complex I-B17 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-AGGG / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-15 kDa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-B14 / Complex I-B15 / NADH:ubiquinone oxidoreductase subunit A9 / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein / Complex I-30kD / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Complex I-B9 / Complex I-B14.5a / Complex I-B18 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.7 / Complex I-SGDH
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKampjut D / Sazanov LA
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Commission665385European Union
European Commission653706European Union
CitationJournal: Science / Year: 2020
Title: The coupling mechanism of mammalian respiratory complex I.
Authors: Domen Kampjut / Leonid A Sazanov /
Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
History
DepositionJun 30, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateNov 11, 2020-
Current statusNov 11, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zkj
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11251.map.gz / Format: CCP4 / Size: 30.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 162 pix.
= 171.882 Å
1.06 Å/pix.
x 184 pix.
= 195.224 Å
1.06 Å/pix.
x 272 pix.
= 288.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.05
Minimum - Maximum-0.12229257 - 0.42623985
Average (Standard dev.)0.002242243 (±0.024289826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions184272162
Spacing162184272
CellA: 171.882 Å / B: 195.224 Å / C: 288.592 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z162184272
origin x/y/z0.0000.0000.000
length x/y/z171.882195.224288.592
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162184272
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS272184162
D min/max/mean-0.1220.4260.002

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Supplemental data

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Sample components

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Entire Complex I with NADH, open3

EntireName: Complex I with NADH, open3 / Number of Components: 59

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Component #1: protein, Complex I with NADH, open3

ProteinName: Complex I with NADH, open3 / Recombinant expression: No
MassExperimental: 1000 kDa
SourceSpecies: Ovis aries (sheep)

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Component #2: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.68775 kDa
SourceSpecies: Sheep (sheep)

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Component #3: protein, Mitochondrial complex I, 24 kDa subunit

ProteinName: Mitochondrial complex I, 24 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.373551 kDa
SourceSpecies: Sheep (sheep)

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Component #4: protein, NADH:ubiquinone oxidoreductase core subunit S1

ProteinName: NADH:ubiquinone oxidoreductase core subunit S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.519297 kDa
SourceSpecies: Sheep (sheep)

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Component #5: protein, Mitochondrial complex I, 49 kDa subunit

ProteinName: Mitochondrial complex I, 49 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.661453 kDa
SourceSpecies: Sheep (sheep)

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Component #6: protein, NADH:ubiquinone oxidoreductase core subunit S3

ProteinName: NADH:ubiquinone oxidoreductase core subunit S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.38457 kDa
SourceSpecies: Sheep (sheep)

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Component #7: protein, Mitochondrial complex I, PSST subunit

ProteinName: Mitochondrial complex I, PSST subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.6229 kDa
SourceSpecies: Sheep (sheep)

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Component #8: protein, Mitochondrial complex I, TYKY subunit

ProteinName: Mitochondrial complex I, TYKY subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.496121 kDa
SourceSpecies: Sheep (sheep)

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Component #9: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.10652 kDa
SourceSpecies: Sheep (sheep)

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Component #10: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.884902 kDa
SourceSpecies: Sheep (sheep)

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Component #11: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.126619 kDa
SourceSpecies: Sheep (sheep)

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Component #12: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.868237 kDa
SourceSpecies: Sheep (sheep)

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Component #13: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.438906 kDa
SourceSpecies: Sheep (sheep)

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Component #14: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.086742 kDa
SourceSpecies: Sheep (sheep)

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Component #15: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.149805 kDa
SourceSpecies: Sheep (sheep)

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Component #16: protein, Mitochondrial complex I, B14.7 subunit

ProteinName: Mitochondrial complex I, B14.7 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.784009 kDa
SourceSpecies: Sheep (sheep)

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Component #17: protein, NADH:ubiquinone oxidoreductase subunit B5

ProteinName: NADH:ubiquinone oxidoreductase subunit B5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.614201 kDa
SourceSpecies: Sheep (sheep)

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Component #18: protein, Acyl carrier protein

ProteinName: Acyl carrier protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.608199 kDa
SourceSpecies: Sheep (sheep)

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Component #19: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.139209 kDa
SourceSpecies: Sheep (sheep)

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Component #20: protein, Mitochondrial complex I, PDSW subunit

ProteinName: Mitochondrial complex I, PDSW subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.880752 kDa
SourceSpecies: Sheep (sheep)

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Component #21: protein, Mitochondrial complex I, 10 kDa subunit

ProteinName: Mitochondrial complex I, 10 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.916529 kDa
SourceSpecies: Sheep (sheep)

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Component #22: protein, Mitochondrial complex I, 13 kDa subunit

ProteinName: Mitochondrial complex I, 13 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.457175 kDa
SourceSpecies: Sheep (sheep)

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Component #23: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.381994 kDa
SourceSpecies: Sheep (sheep)

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Component #24: protein, NADH:ubiquinone oxidoreductase subunit A9

ProteinName: NADH:ubiquinone oxidoreductase subunit A9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.02559 kDa
SourceSpecies: Sheep (sheep)

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Component #25: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.097824 kDa
SourceSpecies: Sheep (sheep)

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Component #26: protein, Mitochondrial complex I, B13 subunit

ProteinName: Mitochondrial complex I, B13 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.287505 kDa
SourceSpecies: Sheep (sheep)

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Component #27: protein, NADH:ubiquinone oxidoreductase subunit A6

ProteinName: NADH:ubiquinone oxidoreductase subunit A6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302812 kDa
SourceSpecies: Sheep (sheep)

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Component #28: protein, Mitochondrial complex I, B14.5a subunit

ProteinName: Mitochondrial complex I, B14.5a subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.701613 kDa
SourceSpecies: Sheep (sheep)

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Component #29: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.115508 kDa
SourceSpecies: Sheep (sheep)

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.557148 kDa
SourceSpecies: Sheep (sheep)

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Component #31: protein, NADH:ubiquinone oxidoreductase subunit S5

ProteinName: NADH:ubiquinone oxidoreductase subunit S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.605594 kDa
SourceSpecies: Sheep (sheep)

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Component #32: protein, NADH:ubiquinone oxidoreductase subunit A3

ProteinName: NADH:ubiquinone oxidoreductase subunit A3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.325851 kDa
SourceSpecies: Sheep (sheep)

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Component #33: protein, NADH:ubiquinone oxidoreductase subunit B3

ProteinName: NADH:ubiquinone oxidoreductase subunit B3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.146679 kDa
SourceSpecies: Sheep (sheep)

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Component #34: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.431655 kDa
SourceSpecies: Sheep (sheep)

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Component #35: protein, NADH:ubiquinone oxidoreductase subunit B4

ProteinName: NADH:ubiquinone oxidoreductase subunit B4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.236375 kDa
SourceSpecies: Sheep (sheep)

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Component #36: protein, Mitochondrial complex I, B16.6 subunit

ProteinName: Mitochondrial complex I, B16.6 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.766461 kDa
SourceSpecies: Sheep (sheep)

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Component #37: protein, Mitochondrial complex I, B17 subunit

ProteinName: Mitochondrial complex I, B17 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.565126 kDa
SourceSpecies: Sheep (sheep)

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Component #38: protein, NADH:ubiquinone oxidoreductase subunit B7

ProteinName: NADH:ubiquinone oxidoreductase subunit B7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.413807 kDa
SourceSpecies: Sheep (sheep)

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Component #39: protein, NADH:ubiquinone oxidoreductase subunit B9

ProteinName: NADH:ubiquinone oxidoreductase subunit B9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.77991 kDa
SourceSpecies: Sheep (sheep)

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Component #40: protein, NADH:ubiquinone oxidoreductase subunit B2

ProteinName: NADH:ubiquinone oxidoreductase subunit B2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.22677 kDa
SourceSpecies: Sheep (sheep)

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Component #41: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.752602 kDa
SourceSpecies: Sheep (sheep)

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Component #42: protein, Mitochondrial complex I, ESSS subunit

ProteinName: Mitochondrial complex I, ESSS subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.41066 kDa
SourceSpecies: Sheep (sheep)

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Component #43: protein, Mitochondrial complex I, KFYI subunit

ProteinName: Mitochondrial complex I, KFYI subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.802174 kDa
SourceSpecies: Sheep (sheep)

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Component #44: protein, Mitochondrial complex I, MNLL subunit

ProteinName: Mitochondrial complex I, MNLL subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.075305 kDa
SourceSpecies: Sheep (sheep)

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Component #45: protein, Mitochondrial complex I, MWFE subunit

ProteinName: Mitochondrial complex I, MWFE subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.211519 kDa
SourceSpecies: Sheep (sheep)

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Component #46: ligand, IRON/SULFUR CLUSTER

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

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Component #47: ligand, FLAVIN MONONUCLEOTIDE

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

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Component #48: ligand, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

LigandName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.665441 kDa

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Component #49: ligand, FE2/S2 (INORGANIC) CLUSTER

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

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Component #50: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Component #51: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Component #52: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

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Component #53: ligand, 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

LigandName: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.322439 kDa

+
Component #54: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

+
Component #55: 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 #56: ligand, ZINC ION

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

+
Component #57: 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 #58: ligand, ADENOSINE MONOPHOSPHATE

LigandName: ADENOSINE MONOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.347221 kDa

+
Component #59: ligand, MYRISTIC ACID

LigandName: MYRISTIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.228371 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 100 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 33612
3D reconstructionSoftware: RELION / Resolution: 3 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: flexible / Target Criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 5LNK
Overall BValue: 50
Output model

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