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Yorodumi- PDB-5ou7: Crystal structure of the Glycoprotein VI loop truncation mutant P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ou7 | ||||||
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Title | Crystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN | ||||||
Components | Platelet glycoprotein VI | ||||||
Keywords | BLOOD CLOTTING / Platelet / glycoprotein / GPVI / collagen-binding / platelet activation | ||||||
Function / homology | Function and homology information collagen receptor activity / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding ...collagen receptor activity / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / platelet activation / platelet aggregation / transmembrane signaling receptor activity / signaling receptor activity / membrane raft / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Feitsma, L.J. / Huizinga, E.G. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: To Be Published Title: Structural insights into collagen-binding by platelet receptor Glycoprotein VI Authors: Feitsma, L.J. / Brondijk, T.H.C. / Jarvis, G. / Hagemans, D. / Bihan, D. / Jerah, N. / Versteeg, M. / Farndale, R.W. / Huizinga, E.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ou7.cif.gz | 295.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ou7.ent.gz | 241.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ou7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ou7_validation.pdf.gz | 858 KB | Display | wwPDB validaton report |
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Full document | 5ou7_full_validation.pdf.gz | 864.9 KB | Display | |
Data in XML | 5ou7_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 5ou7_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/5ou7 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/5ou7 | HTTPS FTP |
-Related structure data
Related structure data | 5ou9C 2gi7S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 2
NCS ensembles :
NCS oper:
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 19719.215 Da / Num. of mol.: 4 / Mutation: -102-105 -131-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GP6 / Cell line (production host): HEK293-EBNA1-S / Production host: Homo sapiens (human) / References: UniProt: Q9HCN6 #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 362 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M phosphate-citrate buffer pH 4.0 40% (v/v) PEG-300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→113.81 Å / Num. obs: 58873 / % possible obs: 95.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3656 / CC1/2: 0.62 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GI7 Resolution: 1.9→113.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.313 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.169 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.189 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→113.81 Å
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Refine LS restraints |
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