[English] 日本語
Yorodumi
- EMDB-9628: FLAG-tagged mouse Wnt3a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9628
TitleFLAG-tagged mouse Wnt3a
Map dataFLAG-tagged mouse Wnt3a
Sample
  • Complex: FLAG-tagged mouse Wnt3a
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 16.9 Å
AuthorsSato C / Takada S / Takada R
CitationJournal: To Be Published
Title: Wnt3a proteins
Authors: Sato C / Takada S
History
DepositionAug 23, 2018-
Header (metadata) releaseAug 28, 2019-
Map releaseAug 28, 2019-
UpdateAug 28, 2019-
Current statusAug 28, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.199
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.199
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9628.png

Downloads & links

-
Map

FileDownload / File: emd_9628.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFLAG-tagged mouse Wnt3a
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 128 pix.
= 245.76 Å		1.92 Å/pix.
x 128 pix.
= 245.76 Å		1.92 Å/pix.
x 128 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.199 / Movie #1: 0.199
Minimum - Maximum-0.41215074 - 0.36059734
Average (Standard dev.)0.007153686 (±0.0380475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.921.921.92
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z245.760245.760245.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ132132232
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.4120.3610.007

-
Supplemental data

-
Sample components

-
Entire : FLAG-tagged mouse Wnt3a

EntireName: FLAG-tagged mouse Wnt3a
Components
  • Complex: FLAG-tagged mouse Wnt3a

-
Supramolecule #1: FLAG-tagged mouse Wnt3a

SupramoleculeName: FLAG-tagged mouse Wnt3a / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mus musculus (house mouse) / Recombinant cell: L cells
Molecular weightExperimental: 150 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.002 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
15.0 mMHEPES
150.0 mMNaClsodium chloride
0.1 mMn-Dodecyl-beta-D-maltoside
StainingType: NEGATIVE / Material: uranyl acetate
Details: Stained using 2% uranyl acetate on carbon-coated grids

-
Electron microscopy

MicroscopeJEOL 100CX
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

-
Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4999
Initial angle assignmentType: OTHER
Details: Echo-correlated three-dimensional reconstruction method with simulated annealing
Final angle assignmentType: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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