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- PDB-1jpl: GGA3 VHS domain complexed with C-terminal peptide from cation-ind... -
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Open data
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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 | ||||||
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![]() | SIGNALING PROTEIN / Protein-peptide complex / VHS domain / DXXLL sorting signal | ||||||
Function / homology | ![]() Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / Golgi to plasma membrane transport / insulin-like growth factor II binding / protein targeting to lysosome / Golgi to plasma membrane protein transport ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / Golgi to plasma membrane transport / insulin-like growth factor II binding / protein targeting to lysosome / Golgi to plasma membrane protein transport / trans-Golgi network transport vesicle / positive regulation by host of viral process / MET receptor recycling / retinoic acid binding / protein localization to cell surface / TBC/RABGAPs / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / negative regulation of amyloid-beta formation / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / phosphatidylinositol binding / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / ubiquitin binding / phosphoprotein binding / intracellular protein transport / clathrin-coated endocytic vesicle membrane / protein destabilization / protein catabolic process / regulation of protein stability / trans-Golgi network / small GTPase binding / positive regulation of protein catabolic process / recycling endosome membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor activity / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Misra, S. / Puertollano, R. / Bonifacino, J.S. / Hurley, J.H. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.5 KB | Display | ![]() |
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PDB format | ![]() | 120.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.8 KB | Display | ![]() |
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Full document | ![]() | 511.3 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
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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.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |