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Yorodumi- PDB-7kjz: crystal structure of PLEKHA7 PH domain biding inositol-tetraphosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kjz | |||||||||
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Title | crystal structure of PLEKHA7 PH domain biding inositol-tetraphosphate | |||||||||
Components | Pleckstrin homology domain-containing family A member 7 | |||||||||
Keywords | CELL ADHESION / PLEKHA7 / PH domain / Pleckstrin homology domain / PIP / inositol-phosphate | |||||||||
Function / homology | Function and homology information zonula adherens maintenance / pore complex assembly / epithelial cell-cell adhesion / zonula adherens / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome ...zonula adherens maintenance / pore complex assembly / epithelial cell-cell adhesion / zonula adherens / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | |||||||||
Authors | Marassi, F.M. / Aleshin, A.E. / Liddington, R.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2021 Title: Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids. Authors: Aleshin, A.E. / Yao, Y. / Iftikhar, A. / Bobkov, A.A. / Yu, J. / Cadwell, G. / Klein, M.G. / Dong, C. / Bankston, L.A. / Liddington, R.C. / Im, W. / Powis, G. / Marassi, F.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kjz.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kjz.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kjz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7kjz_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7kjz_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7kjz_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kjz ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kjz | HTTPS FTP |
-Related structure data
Related structure data | 7kjoSC 7kk7C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 163 - 282 / Label seq-ID: 5 - 124
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-Components
#1: Protein | Mass: 16057.337 Da / Num. of mol.: 2 / Mutation: D175K Source method: isolated from a genetically manipulated source Details: the sequence GPLGS is cloning artifact / Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHA7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IQ23 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: protein in 2.5 mM I(1,3,4,5)P4, 180 mM NaCl, 20 mM Tris, 30 mM BisTris, 0.5 mM TCEP was mixed with 20% PEG 3350, 200 mM Na acetate PH range: 6-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 29, 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: 2.43→52.1 Å / Num. obs: 11134 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.43→2.53 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1136 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KJO Resolution: 2.43→38.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 15.119 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.04 Å2 / Biso mean: 67.678 Å2 / Biso min: 35.03 Å2
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Refinement step | Cycle: final / Resolution: 2.43→38.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3085 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.434→2.497 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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