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- EMDB-9200: Mouse Protocadherin gamma B6 cis mutant V563D on membranes (energ... -

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Basic information

Entry
Database: EMDB / ID: 9200
TitleMouse Protocadherin gamma B6 cis mutant V563D on membranes (energy filtered)
Map dataProtocadherin gamma B6 cis mutant on liposomes
Samplemouse protocadherin Gamma B6 cis mutant V563D on liposomes
  • (mouse protocadherin gamma B6 cis mutant ...) x 2
  • liposomes
SourceMus (mice) / Mus musculus (house mouse)
Methodelectron tomography / cryo EM
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 7, 2018

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Structure visualization

Downloads & links

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Map

FileOn hold (released when the article is published)
Voxel sizeX=Y=Z: 7.04 Å
Density
Minimum - Maximum-0.14761552 - 0.4655733
Average (Standard dev.)0.11592891 (0.03637942)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions13141224374
Origin0.00.0-53.0
Limit1313.01223.0320.0
Spacing12241314374
CellA: 8616.96 Å / B: 9250.56 Å / C: 2632.96 Å
α=β=γ: 90.0 deg.

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Supplemental data

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Sample components

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Entire mouse protocadherin Gamma B6 cis mutant V563D on liposomes

EntireName: mouse protocadherin Gamma B6 cis mutant V563D on liposomes
Details: mutant protocadherin gamma B6 ectodomains are tethered to membranes through binding of C-terminal octa-histidine tags to Ni-NTA lipid head groups presented on the liposome surface.
Number of components: 4

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Component #1: protein, mouse protocadherin Gamma B6 cis mutant V563D on liposomes

ProteinName: mouse protocadherin Gamma B6 cis mutant V563D on liposomes
Details: mutant protocadherin gamma B6 ectodomains are tethered to membranes through binding of C-terminal octa-histidine tags to Ni-NTA lipid head groups presented on the liposome surface.
Recombinant expression: No
SourceSpecies: Mus (mice)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pi alpha
Cell of expression system: human embryonic kidney 293 freestyle

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Component #2: protein, mouse protocadherin gamma B6 cis mutant V563D EC1-6

ProteinName: mouse protocadherin gamma B6 cis mutant V563D EC1-6 / Details: C-terminal octa-hisitidine tag, mutation V563D / Recombinant expression: No
SourceSpecies: Mus (mice)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pi alpha
Cell of expression system: human embryonic kidney 293 freestyle

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Component #3: protein, liposomes

ProteinName: liposomes
Details: liposomes composed of DOPC and DOGS-NTA (8:2 ratio)
Recombinant expression: No
SourceSpecies: Mus (mice)

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Component #4: protein, mouse protocadherin gamma B6 cis mutant V563D

ProteinName: mouse protocadherin gamma B6 cis mutant V563D / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.4
Support filmN/A
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298.15 K / Humidity: 65 % / Details: 2.5 second blot before plunging..

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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: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 0.001 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 54
3D reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software: TOMO3D

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