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- PDB-1ky6: AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ky6 | ||||||
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Title | AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE | ||||||
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![]() | ENDOCYTOSIS/EXOCYTOSIS / PROTEIN-PEPTIDE COMPLEX / ENDOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | ![]() positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / LDL clearance / 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 ...positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / LDL clearance / 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 / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / membrane coat / membrane fission / molecular sequestering activity / clathrin-dependent endocytosis / MHC class II antigen presentation / regulation of hematopoietic stem cell differentiation / clathrin binding / embryonic organ development / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / Notch signaling pathway / Neutrophil degranulation / phosphatidylinositol binding / secretory granule / female pregnancy / intracellular protein transport / Schaffer collateral - CA1 synapse / terminal bouton / cytoplasmic side of plasma membrane / phospholipid binding / kinase binding / endocytosis / disordered domain specific binding / synaptic vesicle / presynapse / presynaptic membrane / cytoplasmic vesicle / postsynapse / postsynaptic membrane / in utero embryonic development / transmembrane transporter binding / endosome / protein domain specific binding / protein-containing complex binding / protein kinase binding / nucleus / plasma membrane / 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.2 KB | Display | ![]() |
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Full document | ![]() | 381.3 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ky7C ![]() 1kydC ![]() 1kyfC ![]() 1kyuC ![]() 1qtpS 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: 764.783 Da / Num. of mol.: 1 / Fragment: RESIDUES 375-381 / Source method: obtained synthetically Details: The peptide was chemically synthesized. It is naturally found in Rattus Norvegicus (Norway Rat) EPSIN 1 References: UniProt: O88339 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.46 % | ||||||||||||||||||||||||||||||||||||
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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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 1999 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 15307 / Num. obs: 15307 / % possible obs: 88.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.181 / % possible all: 62.1 |
Reflection | *PLUS Num. measured all: 52333 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 62.1 % / Rmerge(I) obs: 0.181 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QTP Resolution: 2→19.79 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 379415.85 / Data cutoff high rms absF: 379415.85 / 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: 62.6174 Å2 / ksol: 0.381986 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.186 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / Rfactor Rwork: 0.281 / Rfactor obs: 0.281 |