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- PDB-6qh6: AP2 clathrin adaptor core with two cargo peptides in open+ confor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qh6 | |||||||||
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Title | AP2 clathrin adaptor core with two cargo peptides in open+ conformation | |||||||||
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![]() | PROTEIN TRANSPORT / ENDOCYTOSIS / TRAFFICKING / CELL MEMBRANE | |||||||||
Function / homology | ![]() Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Gap junction degradation / Formation of annular gap junctions ...Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Gap junction degradation / Formation of annular gap junctions / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / MHC class II antigen presentation / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / VLDLR internalisation and degradation / MHC class II antigen presentation / Recycling pathway of L1 / AP-2 adaptor complex / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / maintenance of protein location in cell / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / T cell selection / Retrograde neurotrophin signalling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-coated endocytic vesicle / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / MHC class II protein binding / membrane coat / vesicle budding from membrane / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / MHC class II antigen presentation / coronary vasculature development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / Alpha-defensins / positive regulation of kinase activity / aorta development / negative regulation of protein localization to plasma membrane / regulation of T cell activation / ventricular septum development / Neutrophil degranulation / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / low-density lipoprotein particle receptor binding / clathrin binding / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / regulation of calcium ion transport / positive regulation of receptor internalization / macrophage differentiation / synaptic vesicle endocytosis / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / EPH-ephrin mediated repulsion of cells / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / MHC class II antigen presentation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / VLDLR internalisation and degradation Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wrobel, A.G. / Owen, D.J. / McCoy, A.J. / Evans, P.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation. Authors: Wrobel, A.G. / Kadlecova, Z. / Kamenicky, J. / Yang, J.C. / Herrmann, T. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Martin, S. / Muller, S. / Sroubek, F. / Neuhaus, D. / Honing, S. / Owen, D.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.2 KB | Display | ![]() |
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PDB format | ![]() | 281.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-AP-2 complex subunit ... , 5 types, 5 molecules ABMNS
#1: Protein | Mass: 69642.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 67091.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 51124.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#7: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 2 types, 2 molecules PQ
#5: Protein/peptide | Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: YXXPhi INTERNALISATION SIGNAL MOTIF / Source: (synth.) ![]() |
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#6: Protein/peptide | Mass: 1314.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ACIDIC DILEUCINE INTERNALISATION SIGNAL MOTIF / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.9 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 7.5% PVA, 9% 1-propanol, 90 mM Hepes pH 7.4, 100 mM guanidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.252 Å / Relative weight: 1 |
Reflection | Resolution: 5→91 Å / Num. obs: 15525 / % possible obs: 99.6 % / Redundancy: 4.8 % / CC1/2: 0.942 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.138 / Rrim(I) all: 0.247 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 5→5.59 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 324.42 Å2
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Refinement step | Cycle: 1 / Resolution: 5→91 Å
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