+Open data
-Basic information
Entry | Database: PDB / ID: 7r58 | ||||||
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Title | Crystal structure of the GPVI-glenzocimab complex | ||||||
Components |
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Keywords | BLOOD CLOTTING | ||||||
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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å | ||||||
Authors | Jandrot-Perrus, M. / Lebozec, K. / Rose, N. / Welin, M. / Billiald, P. | ||||||
Funding support | 1items
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Citation | Journal: Blood Adv / Year: 2023 Title: Targeting platelet GPVI with glenzocimab: a novel mechanism for inhibition. Authors: Billiald, P. / Slater, A. / Welin, M. / Clark, J.C. / Loyau, S. / Pugniere, M. / Jiacomini, I.G. / Rose, N. / Lebozec, K. / Toledano, E. / Francois, D. / Watson, S.P. / Jandrot-Perrus, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r58.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r58.ent.gz | 117 KB | Display | PDB format |
PDBx/mmJSON format | 7r58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r58_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 7r58_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 7r58_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 7r58_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r58 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r58 | HTTPS FTP |
-Related structure data
Related structure data | 3gwkS 5azeS 5ou7S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22570.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HCN6 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24250.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
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#3: Antibody | Mass: 24105.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) |
-Non-polymers , 4 types, 788 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-SCN / | #7: 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: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20 % PEG 3350 0.2 M KSCN 0.1 M Bis-Tris propane pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.43 Å / Num. obs: 56379 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.995 / Rpim(I) all: 0.072 / Rrim(I) all: 0.265 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3695 / CC1/2: 0.598 / Rpim(I) all: 0.512 / Rrim(I) all: 1.851 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AZE,3GWK,5OU7 Resolution: 1.902→49.43 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.139
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Displacement parameters | Biso mean: 22.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.902→49.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.92 Å
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