+Open data
-Basic information
Entry | Database: PDB / ID: 6v9g | ||||||
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Title | Kindlin-3 double deletion mutant long form | ||||||
Components | Fermitin family homolog 3 | ||||||
Keywords | BLOOD CLOTTING / integrin binding protein / CELL ADHESION | ||||||
Function / homology | Function and homology information cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway ...cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway / platelet aggregation / integrin binding / Platelet degranulation / positive regulation of cell migration / lipid binding / extracellular exosome / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Xu, Z. / Zhang, T.L. / Xu, Z. / Sun, J.J. / Ding, J.P. / Ma, Y.Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Blood Adv / Year: 2020 Title: Structure basis of the FERM domain of kindlin-3 in supporting integrin alpha IIb beta 3 activation in platelets. Authors: Sun, J. / Xiao, D. / Ni, Y. / Zhang, T. / Cao, Z. / Xu, Z. / Nguyen, H. / Zhang, J. / White, G.C. / Ding, J. / Ma, Y.Q. / Xu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v9g.cif.gz | 346.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v9g.ent.gz | 281.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/6v9g ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v9g | HTTPS FTP |
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-Related structure data
Related structure data | 6v97C 5xpyS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56894.707 Da / Num. of mol.: 2 / Mutation: 166-194 deleted,344-493 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT3, KIND3, MIG2B, URP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UX7 #2: Water | ChemComp-HOH / | Sequence details | The cDNA of human kindlin-3 (Genbank ID: NM_031471) used for expressing kindlin-3 protein in this ...The cDNA of human kindlin-3 (Genbank ID: NM_031471) used for expressing kindlin-3 protein in this study is a short variant, resulting in 4 residues (IPRR) missing when compared to Q86UX7 in Uniprot | |
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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: 3.06 Å3/Da / Density % sol: 59.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium nitrate, 12% PEG3350, 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→47.73 Å / Num. obs: 49776 / % possible obs: 99.6 % / Redundancy: 4.4 % / CC1/2: 0.999 / Net I/σ(I): 20.66 |
Reflection shell | Resolution: 2.35→2.43 Å / Num. unique obs: 4904 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XPY Resolution: 2.35→47.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.828 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.224 / Details: U VALUES : WITH TLS ADDED
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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: 129.76 Å2 / Biso mean: 56.399 Å2 / Biso min: 27.15 Å2
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Refinement step | Cycle: final / Resolution: 2.35→47.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / 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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