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Yorodumi- PDB-6v06: Crystal structure of Beta-2 glycoprotein I purified from plasma (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v06 | |||||||||
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Title | Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI) | |||||||||
Components | Beta-2-glycoprotein 1 | |||||||||
Keywords | BLOOD CLOTTING / PLASMA GLYCOPROTEIN / COAGULATION / INNATE IMMUNE SYSTEM / AUTOIMMUNITY / THROMBOSIS / SUSHI DOMAIN | |||||||||
Function / homology | Function and homology information lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / collagen-containing extracellular matrix / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Chen, Z. / Ruben, E.A. / Planer, W. / Chinnaraj, M. / Zuo, X. / Pengo, V. / Macor, P. / Tedesco, F. / Pozzi, N. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. Authors: Ruben, E. / Planer, W. / Chinnaraj, M. / Chen, Z. / Zuo, X. / Pengo, V. / De Filippis, V. / Alluri, R.K. / McCrae, K.R. / Macor, P. / Tedesco, F. / Pozzi, N. #1: Journal: EMBD J. / Year: 1999 Title: Crystal structure of human beta2-glycoprotein I: implications for phospholipid binding and the antiphospholipid syndrome Authors: Schwarzenbacher, R. / Zeth, K. / Diederichs, K. / Gries, A. / Kostner, G.M. / Laggner, P. / Prassl, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v06.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v06.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v06_validation.pdf.gz | 570.4 KB | Display | wwPDB validaton report |
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Full document | 6v06_full_validation.pdf.gz | 576.1 KB | Display | |
Data in XML | 6v06_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 6v06_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/6v06 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/6v06 | HTTPS FTP |
-Related structure data
Related structure data | 6v08C 6v09C 1c1zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36299.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02749 |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1- ...alpha-D-mannopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1- ...beta-D-mannopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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 |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4) ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-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 , 3 types, 443 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-EPE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 10.61 Å3/Da / Density % sol: 88.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, 1.5 M AmSO4, 20 mM CaCl2 and 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 59497 / % possible obs: 98.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2899 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C1Z Resolution: 2.4→36.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.616 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.141 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.51 Å2 / Biso mean: 65.47 Å2 / Biso min: 28.59 Å2
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Refinement step | Cycle: final / Resolution: 2.4→36.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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