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Open data
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Basic information
Entry | Database: PDB / ID: 4jvw | ||||||
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Title | IgM C4-domain from mouse | ||||||
![]() | Ig mu chain C region secreted form | ||||||
![]() | PROTEIN BINDING / Immunoglobulin M / antibody / oligomerization / Immunoglobulin fold / Receptor | ||||||
Function / homology | ![]() CD22 mediated BCR regulation / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / positive regulation of B cell activation / B cell affinity maturation / humoral immune response mediated by circulating immunoglobulin ...CD22 mediated BCR regulation / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / Cell surface interactions at the vascular wall / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / pre-B cell allelic exclusion / positive regulation of B cell activation / B cell affinity maturation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / regulation of cell morphogenesis / regulation of immunoglobulin production / B cell activation / B cell proliferation / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / positive regulation of B cell proliferation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / MAPK cascade / antibacterial humoral response / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / blood microparticle / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mueller, R. / Graewert, A.M. / Kern, T. / Madl, T. / Peschek, J. / Sattler, M. / Groll, M. / Buchner, J. | ||||||
![]() | ![]() Title: High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation. Authors: Muller, R. / Grawert, M.A. / Kern, T. / Madl, T. / Peschek, J. / Sattler, M. / Groll, M. / Buchner, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.4 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ba8C ![]() 4jvuC ![]() 1jvuS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 12743.415 Da / Num. of mol.: 4 / Fragment: uno residues 324-436 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M HEPES, 15% PEG 8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 15, 2009 |
Radiation | Monochromator: Scanning emission monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 31721 / Num. obs: 31721 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JVU Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.441 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1577 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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