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- EMDB-8704: Negative stain electron microscopy map of human CD22 extracellula... -

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Basic information

Database: EMDB / ID: 8704
TitleNegative stain electron microscopy map of human CD22 extracellular domain
Samplehuman CD22 B-cell receptor
SourceHomo sapiens / human /
Map dataNegative stain EM Map of unliganded human CD22 extracellular domain (d1-d7 Ig domains)
Methodsingle particle reconstruction, at 30 Å resolution
AuthorsJulien JP / Ereno-Orbea J / Sicard T
CitationNat Commun, 2017, 8, 764-764

Nat Commun, 2017, 8, 764-764 Yorodumi Papers
Molecular basis of human CD22 function and therapeutic targeting.
June Ereño-Orbea / Taylor Sicard / Hong Cui / Mohammad T Mazhab-Jafari / Samir Benlekbir / Alba Guarné / John L Rubinstein / Jean-Philippe Julien

DateDeposition: Apr 24, 2017 / Header (metadata) release: Jun 14, 2017 / Map release: Oct 18, 2017 / Last update: Oct 18, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 4.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 4.6
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links


Fileemd_8704.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.7 Å/pix.
= 172.8 Å
64 pix
2.7 Å/pix.
= 172.8 Å
64 pix
2.7 Å/pix.
= 172.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.7 Å
Contour Level:4.6 (by author), 4.6 (movie #1):
Minimum - Maximum0 - 20.382395
Average (Standard dev.)0.15808961 (0.6337833)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 172.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z172.800172.800172.800
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean0.00020.3820.158

Supplemental data

Sample components

Entire human CD22 B-cell receptor

EntireName: human CD22 B-cell receptor / Number of components: 1
MassExperimental: 90 kDa

Component #1: cellular-component, human CD22 B-cell receptor

Cellular-componentName: human CD22 B-cell receptor / Recombinant expression: No
MassExperimental: 90 kDa
SourceSpecies: Homo sapiens / human /
Source (engineered)Expression System: Homo sapiens / human /

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.03 mg/ml / pH: 9
VitrificationCryogen name: NONE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ORIUS SC200 (2k x 2k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6312
3D reconstructionResolution: 30 Å / Resolution method: OTHER

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