[English] 日本語
Yorodumi
- EMDB-9197: Mouse Protocadherin gamma B6 dimer-of-dimers -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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 7, 2018

-
Structure visualization

Downloads & links

-
Map

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions112112112
Origin0.00.00.0
Limit111.0111.0111.0
Spacing112112112
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
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more