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

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Basic information

Entry
Database: EMDB / ID: 8704
TitleNegative stain electron microscopy map of human CD22 extracellular domain
Map dataNegative stain EM Map of unliganded human CD22 extracellular domain (d1-d7 Ig domains)
Samplehuman CD22 B-cell receptor:
Function / homologyImmunoglobulin-like fold / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Immunoglobulin subtype 2 / Immunoglobulin subtype / Immunoglobulin-like domain / CD80-like, immunoglobulin C2-set / Immunoglobulin-like domain superfamily / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Ig-like domain profile. ...Immunoglobulin-like fold / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Immunoglobulin subtype 2 / Immunoglobulin subtype / Immunoglobulin-like domain / CD80-like, immunoglobulin C2-set / Immunoglobulin-like domain superfamily / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Ig-like domain profile. / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / CD22 mediated BCR regulation / carbohydrate binding / cell adhesion / extracellular exosome / integral component of membrane / plasma membrane / B-cell receptor CD22
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 30 Å resolution
AuthorsJulien JP / Ereno-Orbea J / Sicard T
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis of human CD22 function and therapeutic targeting.
Authors: 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

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Structure visualization

Movie
  • 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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean0.00020.3820.158

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Supplemental data

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Sample components

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Entire human CD22 B-cell receptor

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

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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)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.03 mg/ml / pH: 9
VitrificationCryogen name: NONE

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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)

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Image processing

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

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