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- EMDB-8153: Masked monomer of ATP synthase dimer from Yarrowia lipolytica, su... -

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Basic information

Entry
Database: EMDB / ID: EMD-8153
TitleMasked monomer of ATP synthase dimer from Yarrowia lipolytica, subclass 1
Map dataNone
Sample
  • Complex: Fo ATP synthase dimer
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsHahn A / Parey K / Bublitz M / Mills DJ / Zickermann V / Vonck J / Kuehlbrandt W / Meier T
CitationJournal: Mol Cell / Year: 2016
Title: Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology.
Authors: Alexander Hahn / Kristian Parey / Maike Bublitz / Deryck J Mills / Volker Zickermann / Janet Vonck / Werner Kühlbrandt / Thomas Meier /
Abstract: We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 ...We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology.
History
DepositionApr 20, 2016-
Header (metadata) releaseJul 20, 2016-
Map releaseJul 20, 2016-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8153.png

Downloads & links

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Map

FileDownload / File: emd_8153.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 300 pix.
= 489. Å		1.63 Å/pix.
x 300 pix.
= 489. Å		1.63 Å/pix.
x 300 pix.
= 489. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.017231222 - 0.054448895
Average (Standard dev.)-0.00007985883 (±0.0038643454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 489.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z489.000489.000489.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0170.054-0.000

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Supplemental data

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Sample components

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Entire : Fo ATP synthase dimer

EntireName: Fo ATP synthase dimer
Components
  • Complex: Fo ATP synthase dimer

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Supramolecule #1: Fo ATP synthase dimer

SupramoleculeName: Fo ATP synthase dimer / type: complex / ID: 1 / Parent: 0
Details: The Fo section of the F1Fo dimer was masked for refinement
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 1.2 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: 7.5
Details: 30 mM MOPS-NaOH pH 7.5, 2 mM MgCl2, 0.5 mM EDTA, 50 mM NaCl, 0.05% (w/v) digitonin
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 7 to 9 s.

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 2-21 / Number real images: 2500 / Average exposure time: 6.0 sec. / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30675 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 20000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 50118
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

2161


Details: subtomogram average
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3)
Details: The map was masked for reconstruction of one monomer of the F1Fo dimer. Classification indicated 3 states with different orientations of the rotor.
Number images used: 5621
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 12000 / Software - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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