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- EMDB-4385: Cryo-EM structure of respiratory complex I from Yarrowia lipolyti... -

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Basic information

Entry
Database: EMDB / ID: EMD-4385
TitleCryo-EM structure of respiratory complex I from Yarrowia lipolytica under turnover
Map data
Sample
  • Complex: Mitochondrial NADH:ubiquinone oxidoreductase
Function / homology
Function and homology information


lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial iron-sulfur cluster assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / ubiquinone binding ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial iron-sulfur cluster assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / ubiquinone binding / acyl binding / electron transport coupled proton transport / iron-sulfur cluster assembly / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / protein-containing complex binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit ...NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / SLBB domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 / 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 / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / 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 Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / 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 dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / NuoE domain / CHCH domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily
Similarity search - Domain/homology
Complex 1 LYR protein domain-containing protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Acyl carrier protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Thioredoxin-like protein ...Complex 1 LYR protein domain-containing protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Acyl carrier protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Thioredoxin-like protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / Zinc finger CHCC-type domain-containing protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / YALI0D10274p / YALI0E23749p / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / YALI0A17946p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / YALI0E28424p / YALI0E23089p / YALI0E11891p / Acyl carrier protein / YALI0D24585p / YALI0D19030p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / YALI0C03201p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH-ubiquinone oxidoreductase / YALI0A01419p / NUVM protein / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase / Subunit NUHM of protein NADH:Ubiquinone oxidoreductase / NUGM protein / NUCM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.51 Å
AuthorsParey K / Vonck J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research FoundationEXC 115 Germany
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of respiratory complex I at work.
Authors: Kristian Parey / Ulrich Brandt / Hao Xie / Deryck J Mills / Karin Siegmund / Janet Vonck / Werner Kühlbrandt / Volker Zickermann /
Abstract: Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 ...Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
History
DepositionApr 19, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 10, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4385.png

Downloads & links

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Map

FileDownload / File: emd_4385.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.054 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.069257624 - 0.2725249
Average (Standard dev.)0.0000003818563 (±0.004611891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions456456456
Spacing456456456
CellA=B=C: 480.62402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0541.0541.054
M x/y/z456456456
origin x/y/z0.0000.0000.000
length x/y/z480.624480.624480.624
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS456456456
D min/max/mean-0.0690.2730.000

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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
Components
  • Complex: Mitochondrial NADH:ubiquinone oxidoreductase

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Supramolecule #1: Mitochondrial NADH:ubiquinone oxidoreductase

SupramoleculeName: Mitochondrial NADH:ubiquinone oxidoreductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#42
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 963.7 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Component:
ConcentrationFormulaName
20.0 mMTris
100.0 mMNaClSodium chloridesodium cloride
1.0 mMEDTAEthylenediaminetetraacetic acid
0.025 %DDM
GridModel: C-flat-1/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
Details4 uM of complex I incubated with 400 uM DBQ was mixed in the ratio 1:1 with 2 uM bo3-type ubiquinol oxidase, TMV (0.13 mg/ml)and 4 mM NADH

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 113852 / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: -0.0045 µm / Nominal defocus min: -0.0015 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 5964 / Average exposure time: 81.0 sec. / Average electron dose: 35.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 273581
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

4110

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 115083
FSC plot (resolution estimation)

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