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Yorodumi- PDB-1jpl: GGA3 VHS domain complexed with C-terminal peptide from cation-ind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jpl | ||||||
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Title | GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose 6-phosphate receptor | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Protein-peptide complex / VHS domain / DXXLL sorting signal | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / Golgi to plasma membrane protein transport / protein targeting to lysosome / Golgi to plasma membrane transport ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / Golgi to plasma membrane protein transport / protein targeting to lysosome / Golgi to plasma membrane transport / insulin-like growth factor II binding / trans-Golgi network transport vesicle / endocytic recycling / MET receptor recycling / retinoic acid binding / protein localization to cell surface / TBC/RABGAPs / lysosomal transport / Golgi Associated Vesicle Biogenesis / negative regulation of amyloid-beta formation / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / ubiquitin binding / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / intracellular protein transport / protein catabolic process / protein destabilization / regulation of protein stability / trans-Golgi network / small GTPase binding / recycling endosome membrane / positive regulation of protein catabolic process / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / early endosome membrane / spermatogenesis / lysosome / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Amyloid fiber formation / Golgi membrane / focal adhesion / Neutrophil degranulation / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / protein-containing complex / extracellular exosome / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Misra, S. / Puertollano, R. / Bonifacino, J.S. / Hurley, J.H. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains. Authors: Misra, S. / Puertollano, R. / Kato, Y. / Bonifacino, J.S. / Hurley, J.H. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors have gel filtration and analytical ultracentrifugation data that suggest that the asymmetric unit contains 4 biological units (chains A/E, B/F, C/G, D/H). The authors think the apparent dimer in the crystal is due to crystallization. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jpl.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jpl.ent.gz | 120.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jpl ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jpl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 19716.924 Da / Num. of mol.: 4 / Fragment: VHS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GGA3 / Plasmid: pHis-parallel2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZ52 #2: Protein/peptide | Mass: 1457.499 Da / Num. of mol.: 4 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P11717 #3: 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: 2.59 Å3/Da / Density % sol: 52.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.6 Details: 1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 11 / PH range high: 10.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97900, 0.97938, 0.95369 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001 | ||||||||||||
Radiation | Monochromator: Focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→99 Å / Num. all: 34965 / Num. obs: 34790 / % possible obs: 99.5 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 10.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 26.7 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 6.7 / Num. unique all: 3381 / % possible all: 99.3 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.078 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.3 % / Num. unique obs: 3381 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→35.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 253695.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.8533 Å2 / ksol: 0.371704 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→35.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor obs: 0.214 / Rfactor Rfree: 0.258 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.311 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.263 / Rfactor obs: 0.262 |