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Yorodumi- SASDDH2: Aglycosylated Human Immunoglobulin G Fc Region (Aglycosylated hum... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDDH2 |
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Sample | Aglycosylated Human Immunoglobulin G Fc Region
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Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function |
Biological species | Homo sapiens (human) |
Citation | Journal: MAbs / Year: 2019 Title: C2 domain orientation of human immunoglobulin G in solution: Structural comparison of glycosylated and aglycosylated Fc regions using small-angle X-ray scattering. Authors: Seiki Yageta / Hiroshi Imamura / Risa Shibuya / Shinya Honda / Abstract: The N-linked glycan in immunoglobulin G is critical for the stability and function of the crystallizable fragment (Fc) region. Alteration of these protein properties upon the removal of the N-linked ...The N-linked glycan in immunoglobulin G is critical for the stability and function of the crystallizable fragment (Fc) region. Alteration of these protein properties upon the removal of the N-linked glycan has often been explained by the alteration of the C2 domain orientation in the Fc region. To confirm this hypothesis, we examined the small-angle X-ray scattering (SAXS) profile of the glycosylated Fc region (gFc) and aglycosylated Fc region (aFc) in solution. Conformational characteristics of the C2 domain orientation were validated by comparison with SAXS profiles theoretically calculated from multiple crystal structures of the Fc region with different C2 domain orientations. The reduced chi-square values from the fitting analyses of gFc and aFc associated with the degree of openness or closure of each crystal structure, as determined from the first principal component that partially governed the variation of the C2 domain orientation extracted by a singular value decomposition analysis. For both gFc and aFc, the best-fitted SAXS profiles corresponded to ones calculated based on the crystal structure of gFc that formed a "semi-closed" C2 domain orientation. Collectively, the data indicated that the removal of the N-linked glycan only negligibly affected the C2 domain orientation in solution. These findings will guide the development of methodology for the production of highly refined functional Fc variants. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDDH2 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #2722 | Type: atomic / Chi-square value: 0.026 / P-value: 0.010176 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: Aglycosylated Human Immunoglobulin G Fc Region / Specimen concentration: 3.19 mg/ml |
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Buffer | Name: 20 mM Citrate-Phosphate / pH: 7 |
Entity #935 | Name: aFc / Type: protein / Description: Aglycosylated human immunoglobulin G Fc region / Formula weight: 25.651 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: P01857 Sequence: ADKTHTCPPC PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISKA KGQPREPQVY TLPPSREEMT KNQVSLTCLV KGFYPSDIAV EWESNGQPEN ...Sequence: ADKTHTCPPC PAPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISKA KGQPREPQVY TLPPSREEMT KNQVSLTCLV KGFYPSDIAV EWESNGQPEN NYKTTPPVLD SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK SLSLSPGK |
-Experimental information
Beam | Instrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-10C City: Tsukuba / 国: Japan / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 2 mm | |||||||||||||||||||||||||||||||||
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Detector | Name: Pilatus3 2M / Pixsize x: 0.172 mm | |||||||||||||||||||||||||||||||||
Scan | Title: Aglycosylated Human Immunoglobulin G Region / Measurement date: Mar 5, 2017 / Cell temperature: 25 °C / Exposure time: 2 sec. / Number of frames: 15 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 351 /
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Result | Type of curve: single_conc
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