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Yorodumi- PDB-5xmh: Crystal structure of an IgM rheumatoid factor YES8c in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xmh | |||||||||
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Title | Crystal structure of an IgM rheumatoid factor YES8c in complex with IgG1 Fc | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / Complex / Rheumatoid factor / Autoantibody | |||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | |||||||||
Authors | Shiroishi, M. / Shimokawa, K. / Lee, J.M. / Kusakabe, M. / Ueda, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function analyses of a stereotypic rheumatoid factor unravel the structural basis for germline-encoded antibody autoreactivity. Authors: Shiroishi, M. / Ito, Y. / Shimokawa, K. / Lee, J.M. / Kusakabe, T. / Ueda, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xmh.cif.gz | 217.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xmh.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xmh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5xmh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xmh_validation.xml.gz | 38 KB | Display | |
Data in CIF | 5xmh_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xmh ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xmh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 3 types, 6 molecules ABLCHD
#1: Antibody | Mass: 23634.676 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 239-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5 #2: Antibody | Mass: 23625.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #3: Antibody | Mass: 23799.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 1 types, 64 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.81 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, sodium acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 77576 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.355 / Num. unique obs: 3825 / CC1/2: 0.917 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Resolution: 2.8→19.9 Å / Cross valid method: FREE R-VALUE Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Displacement parameters | Biso mean: 52 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.9 Å
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