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Yorodumi- PDB-4iim: Crystal structure of the Second SH3 Domain of ITSN1 bound with a ... -
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-Basic information
Entry | Database: PDB / ID: 4iim | ||||||
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Title | Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide | ||||||
Components |
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Keywords | ENDOCYTOSIS / SH3 Domain / ITSN1 / Structural Genomics Consortium / SGC / protein-peptide complex | ||||||
Function / homology | Function and homology information clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / protein localization / recycling endosome / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / lamellipodium / Clathrin-mediated endocytosis / nuclear envelope / molecular adaptor activity / neuron projection / intracellular signal transduction / calcium ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dong, A. / Guan, X. / Huang, H. / Wernimont, A. / Gu, J. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide Authors: Guan, X. / Dong, A. / Huang, H. / Wernimont, A. / Gu, J. / Sidhu, S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iim.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iim.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 4iim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/4iim ftp://data.pdbj.org/pub/pdb/validation_reports/ii/4iim | HTTPS FTP |
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-Related structure data
Related structure data | 1j3tS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 7883.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN1, ITSN, SH3D1A / Plasmid: pHH0239 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15811 #2: Protein/peptide | Mass: 1441.591 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic sequence #3: Chemical | ChemComp-UNX / #4: 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: 1.82 Å3/Da / Density % sol: 32.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 13540 / Num. obs: 13540 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.03 / Χ2: 0.186 / Net I/σ(I): 28.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J3T Resolution: 1.8→29.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8283 / SU B: 3.253 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1465 / SU Rfree: 0.1453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 64.26 Å2 / Biso mean: 26.3598 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.848 Å / Total num. of bins used: 20
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