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Negative-stain surface of human SorCS2 dimer

by single particle reconstruction, at 27 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3840
TitleNegative-stain surface of human SorCS2 dimer
MapNegative-stain surface of human SorCS2 dimer
SamplehSorCS2
AuthorsMoeller A, Januliene D
DateDeposition: 2017-08-07, Header release: 2017-09-06, Map release: 2017-09-06, Last update: 2017-09-20
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.03, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.03, Imaged by UCSF CHIMERA

Supplemental images
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Related Entries

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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_3840.map.gz ( map file in CCP4 format, 3539 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
3.15 A/pix
= 302.4 A
96 pix
3.15 A/pix
= 302.4 A
96 pix
3.15 A/pix
= 302.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum: -0.04070818 - 0.10535957
Average (Standard dev.): 9.551392E-5 (0.007494955)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
Unit CellA= B= C: 302.40002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.15 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.153.153.15
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0410.1050.000
Annotation DetailsNegative-stain surface of human SorCS2 dimer
Supplement
Images
Images
Sample
NamehSorCS2
Number of Components1
Theoretical Mass0.25MDa
Component #1: protein - hSorCS2
Scientific namehSorCS2
Theoretical Mass0.25 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 10090
Expression system: Mus musculus
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.01 mg/ml
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
SoftwareRelion
Resolution By Author27 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections1738
Download
Data from EMDB
Header (meta data in XML format)emd-3840-v19.xml (5.3 KB)
emd-3840-v20.xml (8.1 KB)
emd-3840.xml (5.3 KB)
Map dataemd_3840.map.gz (3.1 MB)
Imagesemd_3840.png (30.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3840
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.2 KB