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- PDB-1kyf: AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kyf | ||||||
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Title | AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE | ||||||
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![]() | ENDOCYTOSIS/EXOCYTOSIS / PROTEIN-PEPTIDE COMPLEX / ENDOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | ![]() Negative regulation of MET activity / EGFR downregulation / LDL clearance / ubiquitin-dependent endocytosis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Golgi to endosome transport ...Negative regulation of MET activity / EGFR downregulation / LDL clearance / ubiquitin-dependent endocytosis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Golgi to endosome transport / Recycling pathway of L1 / AP-2 adaptor complex / clathrin coat of coated pit / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / endocytic recycling / regulation of hematopoietic stem cell differentiation / ciliary membrane / clathrin-coated vesicle / endosomal transport / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / basal plasma membrane / secretory granule / ubiquitin binding / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / SH3 domain binding / endocytosis / regulation of protein localization / disordered domain specific binding / synaptic vesicle / regulation of cell population proliferation / early endosome membrane / cytoplasmic vesicle / postsynapse / early endosome / cadherin binding / apical plasma membrane / protein domain specific binding / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brett, T.J. / Traub, L.M. / Fremont, D.H. | ||||||
![]() | ![]() Title: Accessory protein recruitment motifs in clathrin-mediated endocytosis. Authors: Brett, T.J. / Traub, L.M. / Fremont, D.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.4 KB | Display | ![]() |
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PDB format | ![]() | 126.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.6 KB | Display | ![]() |
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Full document | ![]() | 423.9 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ky6C ![]() 1ky7C ![]() 1kydC ![]() 1kyuC ![]() 1qtsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27828.676 Da / Num. of mol.: 1 / Fragment: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 650.701 Da / Num. of mol.: 1 / Fragment: RESIDUES 628-632 / Source method: obtained synthetically Details: The peptide was chemically synthesized. It is naturally occuring sequence in Mus musculus (mouse) EPS15 References: UniProt: P42567 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.6 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→50 Å / Num. all: 67213 / Num. obs: 67213 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.059 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.388 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 402957 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.388 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QTS Resolution: 1.22→20 Å / Num. parameters: 19156 / Num. restraintsaints: 22808 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 StereochEM target val spec case: ANISOTROPIC REFINEMENT REDUCED FREE R Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 1897 / Occupancy sum non hydrogen: 2342 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.1543 / Rfactor obs: 0.153 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.153 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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