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Negative-stain surface of SorCS1 monomer

by single particle reconstruction, at 18 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.06, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.06, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3708
TitleNegative-stain surface of SorCS1 monomer
MapNegative stain surface of mSorCS1 monomer
SampleSorCS1
AuthorsMoeller A, Januliene D
DateDeposition: 2017-05-05, Header release: 2017-06-14, Map release: 2017-09-06, Last update: 2017-09-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.06, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.06, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleJ. Mol. Biol., Year 2017
TitleHidden Twins: SorCS Neuroreceptors Form Stable Dimers.
AuthorsDovile Januliene, Arulmani Manavalan, Peter Lund Ovesen, Karen-Marie Pedersen, Søren Thirup, Anders Nykjær, Arne Moeller
Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany; DANDRITE, iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL 32224, USA.
DANDRITE, Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark.
MIND Centre, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.
Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL 32224, USA; DANDRITE, Department of Biomedicine, Aarhus University, Ole Worms Allé 3, 8000 Aarhus C, Denmark.
LinksPubMed: 28827148, PII: S0022-2836(17)30412-6, DOI: 10.1016/j.jmb.2017.08.006
Map
Fileemd_3708.map.gz ( map file in CCP4 format, 88 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
28 pix
6.29 A/pix
= 176.12 A
28 pix
6.29 A/pix
= 176.12 A
28 pix
6.29 A/pix
= 176.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum: -0.06862277 - 0.21573825
Average (Standard dev.): 0.0036887347 (0.01998518)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions282828
Origin-14-14-14
Limit131313
Spacing282828
Unit CellA= B= C: 176.12 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 6.29 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z6.296.296.29
M x/y/z282828
origin x/y/z0.0000.0000.000
length x/y/z176.120176.120176.120
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-14-14-14
NC/NR/NS282828
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0690.2160.004
Annotation DetailsNegative stain surface of mSorCS1 monomer
Supplement
Images
Images
Sample
NameSorCS1
Number of Components1
Experimental Mass0.14MDa
Component #1: protein - SorCS1
Scientific nameSorCS1
Experimental Mass0.14 MDa
Scientific Name of SpeciesMus musculus

NCBI taxonomy10090
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 10029
Expression system: Cricetulus griseus
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 8
Vitrification
Cryogen NameNONE
Imaging
MicroscopeFEI TECNAI SPIRIT
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose8 e/A**2
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorTVIPS TEMCAM-F416 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author18 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections34000
Download
Data from EMDB
Header (meta data in XML format)emd-3708-v19.xml (5.2 KB)
emd-3708-v20.xml (7.5 KB)
emd-3708.xml (5.2 KB)
Map dataemd_3708.map.gz (80.7 KB)
Imagesemd_3708.png (29.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3708
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 27 KB