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- EMDB-8705: Negative stain electron microscopy map of human CD22 extracellula... -

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Basic information

Entry
Database: EMDB / ID: 8705
TitleNegative stain electron microscopy map of human CD22 extracellular domain in complex with epratuzumab Fab
Map dataNegative stain electron microscopy map of CD22 extracellular domain in complex with Fab fragment of epratuzumab
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: 4.79
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.79
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8705.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:4.79 (by author), 4.79 (movie #1):
Minimum - Maximum0 - 15.929847
Average (Standard dev.)0.1983934 (0.70661753)
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/mean0.00015.9300.198

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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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