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- EMDB-9197: Mouse Protocadherin gamma B6 dimer-of-dimers -

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Basic information

Database: EMDB / ID: 9197
TitleMouse Protocadherin gamma B6 dimer-of-dimers
Map datasubtomogram averaged map of Protocadherin gamma B6 EC1-6 dimer-of-dimers in solution
Samplemouse protocadherin gamma b6:
SourceMus (mice) / Mus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / 35 Å resolution
AuthorsBrasch J / Noble AJ / Shapiro L / Carragher B / Potter CS
CitationJournal: Nature
Title: Visualization of clustered protocadherin neuronal self-recognition complexes
Authors: Brasch J / Goodman KM / Noble AJ / Rapp M / Mannepalli S / Bahna F / Dandey VP / Bepler T / Berger B / Maniatis T / Potter CS / Carragher B / Honig B / Shapiro L
DateDeposition: Oct 12, 2018 / Header (metadata) release: Nov 7, 2018 / Last update: Nov 21, 2018

Structure visualization

Downloads & links


FileOn hold (released when the article is published)
Voxel sizeX=Y=Z: 7.04 Å
Contour Level:3.54 (by author)
Minimum - Maximum-5.6383686 - 14.336349
Average (Standard dev.)-0.000000000015159 (0.46186543)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 788.48 Å
α=β=γ: 90.0 deg.

Supplemental data

Sample components

Entire mouse protocadherin gamma b6

EntireName: mouse protocadherin gamma b6 / Number of components: 2

Component #1: protein, mouse protocadherin gamma b6

ProteinName: mouse protocadherin gamma b6 / Recombinant expression: No
MassExperimental: 300 kDa
SourceSpecies: Mus (mice)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pi alpha
Cell of expression system: human embryonic kidney 293 freestyle

Component #2: protein, mouse protocadherin gamma b6

ProteinName: mouse protocadherin gamma b6 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.075 mg/ml / pH: 8
VitrificationInstrument: OTHER / Cryogen name: ETHANE / Temperature: 298.15 K / Humidity: 80 %
Details: homemade nanowire grids. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 506
3D reconstructionAlgorithm: FOURIER SPACE / Software: Dynamo / Resolution: 35 Å / Resolution method: OTHER / Details: FSC 0.143 map to model / Euler angles: sub-volume correlation based alignment

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