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- EMDB-4506: Ovine respiratory complex I FRC poor closed class -

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Basic information

Entry
Database: EMDB / ID: EMD-4506
TitleOvine respiratory complex I FRC poor closed class
Map dataOvine mitochondrial respiratory complex I FRC poor closed class.
Sample
  • Complex: Ovine mitochondrial respiratory complex I
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 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
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4506.png

Downloads & links

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Map

FileDownload / File: emd_4506.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOvine mitochondrial respiratory complex I FRC poor closed class.
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.16300695 - 0.42170584
Average (Standard dev.)0.0000064581 (±0.013395342)
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-0.1630.4220.000

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Supplemental data

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Mask #1

Fileemd_4506_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ovine mitochondrial respiratory complex I FRC poor closed...

Fileemd_4506_half_map_1.map
AnnotationOvine mitochondrial respiratory complex I FRC poor closed class. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ovine mitochondrial respiratory complex I FRC poor closed...

Fileemd_4506_half_map_2.map
AnnotationOvine mitochondrial respiratory complex I FRC poor closed class. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ovine mitochondrial respiratory complex I

EntireName: Ovine mitochondrial respiratory complex I
Components
  • Complex: Ovine mitochondrial respiratory complex I

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Supramolecule #1: Ovine mitochondrial respiratory complex I

SupramoleculeName: Ovine mitochondrial respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#44
Details: ovine mitochondrial respiratory complex I FRC poor closed class
Source (natural)Organism: Ovis aries (sheep) / Organ: Heart / Tissue: Cardiac / Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane
Molecular weightTheoretical: 1.4 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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.25 MNaClsodium chloride
0.02 MHEPES
0.02 %Brij-35

Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
VitrificationCryogen name: PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 1854 / Average exposure time: 2.0 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 100000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 400000
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5lnk

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 11791
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2)
FSC plot (resolution estimation)

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