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Yorodumi- PDB-7yir: Crystal structure of N-terminal PH domain of ARAP3 protein from human -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yir | ||||||
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Title | Crystal structure of N-terminal PH domain of ARAP3 protein from human | ||||||
Components | Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 | ||||||
Keywords | CYTOSOLIC PROTEIN / ARAP3 / PH domain | ||||||
Function / homology | Function and homology information phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / cytoskeleton organization / ruffle / RAC1 GTPase cycle / lamellipodium ...phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / cytoskeleton organization / ruffle / RAC1 GTPase cycle / lamellipodium / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Zhang, Y.J. / Liu, Y.R. / Wu, B. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3. Authors: Zhang, Y. / Ge, L. / Xu, L. / Liu, Y. / Wang, J. / Liu, C. / Zhao, H. / Xing, L. / Wang, J. / Wu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yir.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yir.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yir_validation.pdf.gz | 678 KB | Display | wwPDB validaton report |
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Full document | 7yir_full_validation.pdf.gz | 678.1 KB | Display | |
Data in XML | 7yir_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 7yir_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/7yir ftp://data.pdbj.org/pub/pdb/validation_reports/yi/7yir | HTTPS FTP |
-Related structure data
Related structure data | 7yisC 1uprS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13056.944 Da / Num. of mol.: 1 / Fragment: PH1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3, CENTD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWN8 |
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#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS (pH 6.5), 30% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. obs: 8653 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.099→2.14 Å / Rmerge(I) obs: 0.357 / Num. unique obs: 429 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UPR Resolution: 2.099→33.595 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.69 Å2 / Biso mean: 37.2688 Å2 / Biso min: 16.98 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.099→33.595 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 27.4534 Å / Origin y: -29.2362 Å / Origin z: 0.9186 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 3 through 101) |