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- EMDB-4110: Respiratory complex I of Yarrowia lipolytica -

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Basic information

Entry
Database: EMDB / ID: EMD-4110
TitleRespiratory complex I of Yarrowia lipolytica
Map datarespiratory complex I of Yarrowia lipolytica
Sample
  • Complex: NADH:ubiquinone oxidoreductase
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsD'Imprima E / Mills DJ / Parey K / Brandt U / Kuehlbrandt W / Zickermann V / Vonck J
CitationJournal: Biochim Biophys Acta / Year: 2016
Title: Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism.
Authors: Edoardo D'Imprima / Deryck J Mills / Kristian Parey / Ulrich Brandt / Werner Kühlbrandt / Volker Zickermann / Janet Vonck /
Abstract: Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved ...Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy. Our density map at 7.9Å resolution closely matches the 3.6-3.9Å X-ray structure of the Yarrowia lipolytica complex. However, the cryo-EM map indicated an additional subunit on the side of the matrix arm above the membrane surface, pointing away from the membrane arm. The density, which is not present in any previously described complex I structure and occurs in about 20 % of the particles, was identified as the accessory sulfur transferase subunit ST1. The Yarrowia lipolytica complex I preparation is active in generating HS from the cysteine derivative 3-mercaptopyruvate, catalyzed by ST1. We thus provide evidence for a link between respiratory complex I and mitochondrial sulfur metabolism.
History
DepositionOct 14, 2016-
Header (metadata) releaseNov 9, 2016-
Map releaseNov 9, 2016-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.085
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.085
  • 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_4110.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrespiratory complex I of Yarrowia lipolytica
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.085 / Movie #1: 0.085
Minimum - Maximum-0.036020786 - 0.20733824
Average (Standard dev.)0.0003321663 (±0.014732352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z396.480396.480396.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0360.2070.000

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Supplemental data

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Sample components

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Entire : NADH:ubiquinone oxidoreductase

EntireName: NADH:ubiquinone oxidoreductase
Components
  • Complex: NADH:ubiquinone oxidoreductase

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Supramolecule #1: NADH:ubiquinone oxidoreductase

SupramoleculeName: NADH:ubiquinone oxidoreductase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 1 MDa

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
30.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: Before glow discharge the grids were pretreated in chloroform for 1-2 hrs
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: The samples were blotted for 8-10 seconds.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.5 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-24 / Number real images: 2250 / Average exposure time: 1.5 sec. / Average electron dose: 84.0 e/Å2
Details: Images were collected in movi-mode at 17 frames per second
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 50314 / Details: particles were selected manually
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER
Details: A map was calculated from an undeposited x-ray structure of the same molecule
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 7
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 29125
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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