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Yorodumi- PDB-4wjw: Crystal Structure of the Chs5-Chs6 Exomer Cargo Adaptor Complex B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wjw | |||||||||
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Title | Crystal Structure of the Chs5-Chs6 Exomer Cargo Adaptor Complex Bound to portion of Chs3 | |||||||||
Components |
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Keywords | transport protein/transferase / Adaptor protein / cargo binding / vesicular trafficking / chitin synthase / Biosynthetic Protein / transport protein-transferase complex | |||||||||
Function / homology | Function and homology information : / exomer complex / protein localization to bud neck / : / conjugation with cellular fusion / chitosome / chitin synthase / chitin synthase activity / prospore membrane / ascospore wall assembly ...: / exomer complex / protein localization to bud neck / : / conjugation with cellular fusion / chitosome / chitin synthase / chitin synthase activity / prospore membrane / ascospore wall assembly / cellular bud site selection / incipient cellular bud site / Golgi to plasma membrane transport / cellular bud neck / cell septum / mating projection tip / cell periphery / cytoplasmic vesicle membrane / trans-Golgi network / small GTPase binding / protein transport / membrane => GO:0016020 / protein dimerization activity / regulation of DNA-templated transcription / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Weiskoff, A.M. / Fromme, J.C. | |||||||||
Citation | Journal: Front Cell Dev Biol / Year: 2014 Title: Distinct N-terminal regions of the exomer secretory vesicle cargo Chs3 regulate its trafficking itinerary. Authors: Weiskoff, A.M. / Fromme, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wjw.cif.gz | 318.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wjw.ent.gz | 259 KB | Display | PDB format |
PDBx/mmJSON format | 4wjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wjw_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 4wjw_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 4wjw_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 4wjw_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/4wjw ftp://data.pdbj.org/pub/pdb/validation_reports/wj/4wjw | HTTPS FTP |
-Related structure data
Related structure data | 4gns S: Starting model for refinement |
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Similar structure data |
-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: 8653.009 Da / Num. of mol.: 1 / Fragment: unp residues 1-77 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CHS5, CAL3, YLR330W, L8543.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12114 |
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#2: Protein | Mass: 87977.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CHS6, CSD3, YJL099W, J0838 / Production host: Escherichia coli (E. coli) / References: UniProt: P40955 |
#3: Protein/peptide | Mass: 2348.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29465*PLUS, chitin synthase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.3 M AMMONIUM SULFATE, 0.1 M CITRIC ACID / PH range: 4.0-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→44.65 Å / Num. obs: 59936 / % possible obs: 99 % / Redundancy: 12.2 % / Rsym value: 0.09 / Net I/σ(I): 19.45 |
Reflection shell | Resolution: 2.59→2.683 Å / % possible all: 99 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GNS 4gns Resolution: 2.59→44.65 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→44.65 Å
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LS refinement shell |
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