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- EMDB-4507: Ovine respiratory complex I FRC poor open class -

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Basic information

Entry
Database: EMDB / ID: EMD-4507
TitleOvine respiratory complex I FRC poor open class
Map data
SampleOvine mitochondrial respiratory complex I
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsLetts JA / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 27, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • 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_4507.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 512 pix.
= 716.8 Å
1.4 Å/pix.
x 512 pix.
= 716.8 Å
1.4 Å/pix.
x 512 pix.
= 716.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.14985788 - 0.49769443
Average (Standard dev.)0.00001083369 (±0.012568832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 716.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z716.800716.800716.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1500.4980.000

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Supplemental data

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Segmentation: #1

Fileemd_4507_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: ovine mitochondrial respiratory complex I poor open class....

Fileemd_4507_half_map_1.map
Annotationovine mitochondrial respiratory complex I poor open class. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: ovine mitochondrial respiratory complex I poor open class....

Fileemd_4507_half_map_2.map
Annotationovine mitochondrial respiratory complex I poor open class. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ovine mitochondrial respiratory complex I

EntireName: Ovine mitochondrial respiratory complex I
Details: Poor open class from ovine mitochondrial respiratory complex I
Number of Components: 1

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Component #1: protein, Ovine mitochondrial respiratory complex I

ProteinName: Ovine mitochondrial respiratory complex I
Details: Poor open class from ovine mitochondrial respiratory complex I
Recombinant expression: No
MassTheoretical: 1.4 MDa
SourceSpecies: Ovis aries (sheep)
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane / Organ Or Tissue: Heart

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL
Buffer solution: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: PROPANE / Temperature: 277 K / Humidity: 95 %
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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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 e/Å2 / Illumination Mode: OTHER
LensMagnification: 100000 X (calibrated) / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 1854

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 11191
3D reconstructionSoftware: RELION / Resolution: 7.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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