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- EMDB-3840: Negative-stain surface of human SorCS2 dimer -

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Basic information

Entry
Database: EMDB / ID: 3840
TitleNegative-stain surface of human SorCS2 dimer
SamplehSorCS2
SourceHomo sapiens / human
Map dataNegative-stain surface of human SorCS2 dimer
Methodsingle particle reconstruction, at 27 Å resolution
AuthorsMoeller A / Januliene D
CitationJ. Mol. Biol., 2017, 429, 2907-2917

J. Mol. Biol., 2017, 429, 2907-2917 Yorodumi Papers
Hidden Twins: SorCS Neuroreceptors Form Stable Dimers.
Dovile Januliene / Arulmani Manavalan / Peter Lund Ovesen / Karen-Marie Pedersen / Søren Thirup / Anders Nykjær / Arne Moeller

DateDeposition: Aug 7, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Sep 6, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3840.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
3.15 Å/pix.
= 302.4 Å
96 pix
3.15 Å/pix.
= 302.4 Å
96 pix
3.15 Å/pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.15 Å
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)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
CellA=B=C: 302.40002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0410.1050.000

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Supplemental data

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Sample components

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Entire hSorCS2

EntireName: hSorCS2 / Number of components: 1
MassTheoretical: 250 kDa

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Component #1: protein, hSorCS2

ProteinName: hSorCS2 / Recombinant expression: No
MassTheoretical: 250 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1738
3D reconstructionSoftware: RELION / Resolution: 27 Å / Resolution method: FSC 0.143 CUT-OFF

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