+Open data
-Basic information
Entry | Database: PDB / ID: 1lf8 | ||||||
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Title | Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / VHS domain / Protein-phosphopeptide complex | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Kato, Y. / Misra, S. / Puertollano, R. / Hurley, J.H. / Bonifacino, J.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Phosphoregulation of sorting signal-VHS domain interactions by a direct electrostatic mechanism. Authors: Kato, Y. / Misra, S. / Puertollano, R. / Hurley, J.H. / Bonifacino, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lf8.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lf8.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lf8 ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lf8 | HTTPS FTP |
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-Related structure data
Related structure data | 1juqS 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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2 |
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3 |
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4 |
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Unit cell |
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Details | Each VHS domain/phosphopeptide complex corresponds to a single biological unit. There are the equivalent of 4 biological complexes per asymmetric unit. The apparent VHS domain dimer is likely a crystallization artifact. |
-Components
#1: Protein | Mass: 19482.451 Da / Num. of mol.: 4 / Fragment: VHS domain (residues 1-166) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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: 1537.478 Da / Num. of mol.: 4 / Fragment: C-terminus (residues 2480-2491) / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (Human). 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: 2.61 Å3/Da / Density % sol: 52.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM CAPS 10.2-11.0, 200 mM Lithium Sulfate, 1.3-2M Sodium/Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2001 / Details: Osmic Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 37720 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3550 / % possible all: 91.5 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 91.5 % / Rmerge(I) obs: 0.356 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1JUQ Resolution: 2.3→89.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 713707.58 / 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: 42.6607 Å2 / ksol: 0.338167 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→89.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.322 / Rfactor Rwork: 0.264 |