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- EMDB-3546: Structure of a novel N-type ATPase rotor ring (c17) from Burkhold... -

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Basic information

Entry
Database: EMDB / ID: 3546
TitleStructure of a novel N-type ATPase rotor ring (c17) from Burkholderia pseudomallei
SampleRotor ring of the N-type ATPase from B. pseudomallei
SourceBurkholderia pseudomallei / bacteria / バークホルデリア・シュードマレイ, 類鼻疽菌
Map data
Methodsingle particle reconstruction, at 6.1 Å resolution
AuthorsWilkes M / Schulz S / Mills DJ / Kuhlbrandt W / Meier T
CitationEMBO Rep., 2017, 18, 526-535

EMBO Rep., 2017, 18, 526-535 StrPapers
Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei.
Sarah Schulz / Martin Wilkes / Deryck J Mills / Werner Kühlbrandt / Thomas Meier

DateDeposition: Dec 20, 2016 / Header (metadata) release: Jan 25, 2017 / Map release: Mar 8, 2017 / Last update: Apr 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0153
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0153
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3546.map.gz (map file in CCP4 format, 10977 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
1.14 Å/pix.
= 159.6 Å
140 pix
1.14 Å/pix.
= 159.6 Å
140 pix
1.14 Å/pix.
= 159.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.14 Å
Density
Contour Level:0.0153 (by author), 0.0153 (movie #1):
Minimum - Maximum-0.0068107103 - 0.026608359
Average (Standard dev.)0.0010935114 (0.003168713)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin000
Limit139139139
Spacing140140140
CellA=B=C: 159.59999 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z159.600159.600159.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0070.0270.001

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Supplemental data

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Sample components

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Entire Rotor ring of the N-type ATPase from B. pseudomallei

EntireName: Rotor ring of the N-type ATPase from B. pseudomallei
Details: We determined the molecular architecture of the N-type ATPase rotor ring in the melioidosis-causing bacterium Burkholderia pseudomallei by electron cryo-microscopy. The structure shows an unusually large c-ring rotor with 17 subunits that, in the acidic environment of the host phagosome, is driven predominantly by protons.
Number of components: 1

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Component #1: protein, Rotor ring of the N-type ATPase from B. pseudomallei

ProteinName: Rotor ring of the N-type ATPase from B. pseudomallei
Details: We determined the molecular architecture of the N-type ATPase rotor ring in the melioidosis-causing bacterium Burkholderia pseudomallei by electron cryo-microscopy. The structure shows an unusually large c-ring rotor with 17 subunits that, in the acidic environment of the host phagosome, is driven predominantly by protons.
Recombinant expression: No
SourceSpecies: Burkholderia pseudomallei / bacteria / バークホルデリア・シュードマレイ, 類鼻疽菌
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pt7-7

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 4.1 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C17 (17 fold cyclic) / Number of projections: 47000
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF

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