+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8466 | |||||||||
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Title | Human Myeloma IgG4 Structure | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 32.0 Å | |||||||||
Authors | Ryazantsev S / Tischenko V / Zavyalov V | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8466.map.gz | 23.5 MB | EMDB map data format | |
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Header (meta data) | emd-8466-v30.xml emd-8466.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_8466.png emd_8466_1.png emd_8466_2.png | 170.2 KB 170.2 KB 41.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8466 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8466 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8466.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human myeloma IgG4
Entire | Name: human myeloma IgG4 |
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Components |
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-Supramolecule #1: human myeloma IgG4
Supramolecule | Name: human myeloma IgG4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Isolated from the serum and purified to 96% purity |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: blood/serum |
Molecular weight | Experimental: 160 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.8 / Component - Concentration: 20.0 mM / Component - Name: ammonium acetate |
Staining | Type: NEGATIVE / Material: 1% uranyl acetate Details: Negative staining with uranyl acetate was carried out using the approach described by Valentine et al. with modification. |
Grid | Model: Homemade / Material: COPPER / Mesh: 150 / Support film - Material: CARBON / Support film - topology: HOLEY |
Details | Human myeloma IgG4 |
-Electron microscopy
Microscope | JEOL 100CX |
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Electron beam | Acceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 80000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.9 mm |
Sample stage | Specimen holder model: JEOL |
Details | images were close to focus |
Image recording | Film 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 |
-Image processing
Particle selection | Number selected: 1500 Details: We boxed particles with 0.158 nm/pix and box size 196x196 pixels. |
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CTF correction | Details: Images were close to focus, no CTF correction implemented |
Startup model | Type 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 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: EMAN (ver. 2) / Details: EMAN2 system |
Final reconstruction | Applied 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 |
Details | Grids 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. |