[English] 日本語
![](img/lk-miru.gif)
- PDB-2j6e: Crystal Structure of an Autoimmune Complex between a Human IgM Rh... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2j6e | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of an Autoimmune Complex between a Human IgM Rheumatoid Factor and IgG1 Fc reveals a Novel Fc Epitope and Evidence for Affinity Maturation | |||||||||||||||
![]() |
| |||||||||||||||
![]() | IMMUNE SYSTEM / AUTOIMMUNE COMPLEX HUMAN IGM RHEUMATOID FACTOR IGG1-FC / IMMUNOGLOBULIN C REGION / MEMBRANE / GLYCOPROTEIN / TRANSMEMBRANE / HYPOTHETICAL PROTEIN / IMMUNOGLOBULIN DOMAIN | |||||||||||||||
Function / homology | ![]() Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / 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 / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Duquerroy, S. / Stura, E.A. / Bressanelli, S. / Browne, H. / Beale, D. / Hamon, M. / Casali, P. / Vaney, M.C. / Rey, F.A. / Sutton, B.J. / Taussig, M.J. | |||||||||||||||
![]() | ![]() Title: Crystal structure of a human autoimmune complex between IgM rheumatoid factor RF61 and IgG1 Fc reveals a novel epitope and evidence for affinity maturation. Authors: Duquerroy, S. / Stura, E.A. / Bressanelli, S. / Fabiane, S.M. / Vaney, M.C. / Beale, D. / Hamon, M. / Casali, P. / Rey, F.A. / Sutton, B.J. / Taussig, M.J. | |||||||||||||||
History |
| |||||||||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 272 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 4 molecules HILM
#2: Antibody | Mass: 24831.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 24757.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 26140.613 Da / Num. of mol.: 2 / Fragment: FC DOMAIN, RESIDUES 99-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 6 types, 98 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CD / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#6: Chemical | #7: Chemical | ChemComp-CAC / | #8: Chemical | ChemComp-MPD / ( #9: Chemical | ChemComp-ACT / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 52.1 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% MPEG 5000, 3 MM ZINC ACETATE, 3 MM CDCL2, 100 MM SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 36545 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1DN2, 2FB4 Resolution: 3→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 26.6436 Å2 / ksol: 0.249712 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.434 Å / Luzzati d res low obs: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|