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- EMDB-8466: Human Myeloma IgG4 Structure -

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Basic information

Entry
Database: EMDB / ID: EMD-8466
TitleHuman Myeloma IgG4 Structure
Map dataNone
Sample
  • Organelle or cellular component: human myeloma IgG4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 32.0 Å
AuthorsRyazantsev S / Tischenko V / Zavyalov V
CitationJournal: Mol Immunol / Year: 2017
Title: Human myeloma IgG4 reveals relatively rigid asymmetric Y-like structure with different conformational stability of C2 domains.
Authors: Vladimir M Tischenko / Vladimir P Zav'yalov / Sergey N Ryazantsev /
Abstract: Human IgG4 (hIgG4) has weak pro-inflammatory activity. The structural basis for this is still unclear. Here a 3D model of myeloma hIgG4 was created at ∼3nm resolution using electron microscopy (EM) ...Human IgG4 (hIgG4) has weak pro-inflammatory activity. The structural basis for this is still unclear. Here a 3D model of myeloma hIgG4 was created at ∼3nm resolution using electron microscopy (EM) with negative staining and single-particle 3D reconstruction. The hIgG4 model reveals relatively rigid asymmetric Y-like structure. The model shows that one Fab subunit is closer to the upper portion of the Fc subunit (C2 domain) than the other Fab. This is in agreement with X-ray crystallography and X-ray/neutron scattering, recently published by others. The same hIgG4 sample was studied with differential scanning calorimetry (DSC) and fluorescence. The thermodynamics and fluorescence observations indicate that one C2 domain displays less conformational stability than the other. This finding is consistent with the flipping of one C2 domain, observed in pembrolizumab (recombinant hIgG4) by X-ray crystallography. The specific feature of hIgG4 C2 domains together with relatively rigid asymmetric Y-like structure, in which one Fab subunit is closer to the upper portion of the Fc subunit (C2 domain) than the other Fab, can explain the unique biological properties of hIgG4, such as its weak pro-inflammatory activity.
History
DepositionNov 1, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseFeb 14, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.778
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.778
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8466.png

emd_8466_1.png

emd_8466_2.png

Downloads & links

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Map

FileDownload / File: emd_8466.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 196 pix.
= 196. Å		1 Å/pix.
x 196 pix.
= 196. Å		1 Å/pix.
x 196 pix.
= 196. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.778 / Movie #1: 0.778
Minimum - Maximum-1.7277092 - 1.9802194
Average (Standard dev.)0.01634556 (-)
SymmetrySpace group: 0
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 196.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z196196196
origin x/y/z-98.000-98.000-98.000
length x/y/z196.000196.000196.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-1.7281.9800.016

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Supplemental data

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Sample components

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Entire : human myeloma IgG4

EntireName: human myeloma IgG4
Components
  • Organelle or cellular component: human myeloma IgG4

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Supramolecule #1: human myeloma IgG4

SupramoleculeName: human myeloma IgG4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Isolated from the serum and purified to 96% purity
Source (natural)Organism: Homo sapiens (human) / Tissue: blood/serum
Molecular weightExperimental: 160 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.8 / Component - Concentration: 20.0 mM / Component - Name: ammonium acetate
StainingType: NEGATIVE / Material: 1% uranyl acetate
Details: Negative staining with uranyl acetate was carried out using the approach described by Valentine et al. with modification.
GridModel: Homemade / Material: COPPER / Mesh: 150 / Support film - Material: CARBON / Support film - topology: HOLEY
DetailsHuman myeloma IgG4

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Electron microscopy

MicroscopeJEOL 100CX
Detailsimages were close to focus
Image recordingFilm or detector model: KODAK 4489 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average exposure time: 1.5 sec. / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 80000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.9 mm
Sample stageSpecimen holder model: JEOL

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Image processing

DetailsGrids were analyzed in JEM100C (JEOL, Japan) transmission electron microscope at magnification x80000. EM plates with images were scanned using Nikon Cool SuperScan 9000 scanner at 0.158 nm/pix.
Particle selectionNumber selected: 1500
Details: We boxed particles with 0.158 nm/pix and box size 196x196 pixels.
CTF correctionDetails: Images were close to focus, no CTF correction implemented
Startup modelType of model: OTHER
Details: features ellipsoid (2:1) was used as initial model in the first round, than model obtained in the first step were used for 3D reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 2) / Number images used: 1000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2) / Details: EMAN2 system

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