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- EMDB-1542: Three-dimensional structure of Pyrococcus furiosus A1Ao ATP synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-1542
TitleThree-dimensional structure of Pyrococcus furiosus A1Ao ATP synthase
Map datavolume of Pyrococcus furiosus A-type ATP synthase
Sample
  • Sample: A1Ao ATP synthase from Pyrococcus furiosus
  • Protein or peptide: A1Ao ATP synthase
  • Protein or peptide: A1Ao ATP synthase
KeywordsATP synthase / A1Ao ATP synthase
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsVonck J / Pisa KY / Morgner N / Brutschy B / Mueller V
CitationJournal: J Biol Chem / Year: 2009
Title: Three-dimensional structure of A1A0 ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus by electron microscopy.
Authors: Janet Vonck / Kim Y Pisa / Nina Morgner / Bernhard Brutschy / Volker Müller /
Abstract: The archaeal ATP synthase is a multisubunit complex that consists of a catalytic A(1) part and a transmembrane, ion translocation domain A(0). The A(1)A(0) complex from the hyperthermophile ...The archaeal ATP synthase is a multisubunit complex that consists of a catalytic A(1) part and a transmembrane, ion translocation domain A(0). The A(1)A(0) complex from the hyperthermophile Pyrococcus furiosus was isolated. Mass analysis of the complex by laser-induced liquid bead ion desorption (LILBID) indicated a size of 730 +/- 10 kDa. A three-dimensional map was generated by electron microscopy from negatively stained images. The map at a resolution of 2.3 nm shows the A(1) and A(0) domain, connected by a central stalk and two peripheral stalks, one of which is connected to A(0), and both connected to A(1) via prominent knobs. X-ray structures of subunits from related proteins were fitted to the map. On the basis of the fitting and the LILBID analysis, a structural model is presented with the stoichiometry A(3)B(3)CDE(2)FH(2)ac(10).
History
DepositionAug 15, 2008-
Header (metadata) releaseAug 18, 2008-
Map releaseJun 15, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1542.gif

Downloads & links

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Map

FileDownload / File: emd_1542.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationvolume of Pyrococcus furiosus A-type ATP synthase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.77 Å/pix.
x 80 pix.
= 381.6 Å		4.77 Å/pix.
x 80 pix.
= 381.6 Å		4.77 Å/pix.
x 80 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.77 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.3 / Movie #1: 1
Minimum - Maximum-6.37055 - 10.957700000000001
Average (Standard dev.)-0.00000000065542 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 381.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.774.774.77
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z381.600381.600381.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-120-120-120
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-6.37110.958-0.000

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Supplemental data

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Sample components

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Entire : A1Ao ATP synthase from Pyrococcus furiosus

EntireName: A1Ao ATP synthase from Pyrococcus furiosus
Components
  • Sample: A1Ao ATP synthase from Pyrococcus furiosus
  • Protein or peptide: A1Ao ATP synthase
  • Protein or peptide: A1Ao ATP synthase

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Supramolecule #1000: A1Ao ATP synthase from Pyrococcus furiosus

SupramoleculeName: A1Ao ATP synthase from Pyrococcus furiosus / type: sample / ID: 1000 / Oligomeric state: nine different subunits / Number unique components: 9
Molecular weightExperimental: 738 KDa / Theoretical: 738 KDa / Method: LILBID mass spectroscopy

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Macromolecule #1: A1Ao ATP synthase

MacromoleculeName: A1Ao ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATP synthase / Oligomeric state: heteromultimer / Recombinant expression: No
Source (natural)Organism: Pyrococcus furiosus (archaea) / Cell: archaeon / Location in cell: plasma membrane
Molecular weightExperimental: 738 KDa / Theoretical: 738 KDa

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Macromolecule #2: A1Ao ATP synthase

MacromoleculeName: A1Ao ATP synthase / type: protein_or_peptide / ID: 2 / Name.synonym: ATP synthase / Recombinant expression: No
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightExperimental: 738 KDa / Theoretical: 738 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 50 mM this/HCl, 5 mM MgCl2, 10% glycerol, 50 mM KCl, 0.1% Triton-X100, 0.1 mM PMSF
StainingType: NEGATIVE
Details: a drop of 1% (w/v) uranyl acetate was added to a carbon-coated grid with absorbed protein and blotted after 30 s.
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 160,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 51 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 44000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 45000
Sample stageSpecimen holder: eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12912
Final two d classificationNumber classes: 392

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