|Entry||Database: EMDB / ID: 5319|
|Title||Three-dimensional structure of bovine respirasome by single particle cryo-electron tomography|
|Map data||EM map of respirasome from bovine mitochondria|
|Sample||Respirasome from bovine mitochondria:|
|Keywords||Oxidative phosphorylation / mitochondria|
|Source||Bos taurus (cattle)|
|Method||subtomogram averaging / cryo EM / negative staining / 22 Å resolution|
|Authors||Dudkina NV / Kudryashev M / Stahlberg H / Boekema EJ|
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011|
Title: Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography.
Authors: Natalya V Dudkina / Mikhail Kudryashev / Henning Stahlberg / Egbert J Boekema
|Date||Deposition: Jul 5, 2011 / Header (metadata) release: Jul 13, 2011 / Map release: Aug 31, 2011 / Last update: Sep 7, 2011|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5319.map.gz (map file in CCP4 format, 8193 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.8 Å|
CCP4 map header:
-Entire Respirasome from bovine mitochondria
|Entire||Name: Respirasome from bovine mitochondria|
Details: The sample was thawed from storage at -80 degrees Celcius before being loaded onto the grid.
Number of components: 1
Oligomeric State: One monomer of NADH dehydrogenase binds to one dimer of cytochrome bc1 and one monomer of cytochrome c oxidase
|Mass||Theoretical: 1.7 MDa / Experimental: 1.7 MDa / Measured by: blue-native gel electrophoresis|
-Component #1: protein, respirasome
|Protein||Name: respirasome / a.k.a: respirasome / Oligomeric Details: monomer / Details: Solubilized with digitonin / Recombinant expression: No / Number of Copies: 1|
|Mass||Theoretical: 1.7 MDa / Experimental: 1.7 MDa|
|Source||Species: Bos taurus (cattle) / Strain: wild type|
|Source (natural)||Organelle: mitochondrion / Location in cell: inner mitochondrial membrane / Cell: heart muscle cells / Organ or tissue: heart|
|Specimen||Specimen state: particle / Method: negative staining, cryo EM|
|Sample solution||Specimen conc.: 0.5 mg/ml|
Buffer solution: 25 mM Tricine, 7.5 mM Bis-Tris, 0.1 mM PMSF, 0.01% digitonin
|Support film||200 mesh copper Quantifoil grids with an additional carbon support film|
|Staining||2.5 microliters were mixed with 10-nm gold particles as fiducial markers and applied on glow-discharged 200 mesh Quantifoil support grids with an additional carbon support film. Grids were blotted at 100% humidity for 4-6 seconds at a blot offset (the longitudinal grid positioning) setting of -3.5, using a Vitrobot Mk3 (FEI).|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: Blot for 4-6 seconds before plunging / Details: Vitrification instrument: Vitrobot Mk3 (FEI)|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Mar 1, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 80 e/Å2 / Electron beam tilt params: 0 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 34000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 34,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 nm / Energy filter: FEI / Energy window: 0-20 eV
|Specimen Holder||Holder: Multispecimen holder / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: -70 - 70 deg. / Temperature: 77 K ( 15 - K)|
|Camera||Detector: GENERIC GATAN (2k x 2k)|
|Image acquisition||Number of digital images: 21 / Sampling size: 0.38 microns|
|Processing||Method: subtomogram averaging|
Details: The particles were selected from the tomograms by cross-correlation to an artificial globular reference followed by manual selection of particle volumes. Average number of projections used in the 3D reconstructions: 2466. Average number of class averages: 1.
|3D reconstruction||Algorithm: 60 sections of 6 nm thickness / Software: IMOD, XMIPP, AV3 / Resolution: 22 Å / Resolution method: the 0.5 information threshold criterion|
-Atomic model buiding
|Modeling #1||Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 1BGY
|Modeling #2||Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 1OCC
|Modeling #3||Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body|
Input PDB model: 3M9S
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