[English] 日本語
Yorodumi- PDB-6qh6: AP2 clathrin adaptor core with two cargo peptides in open+ confor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qh6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | AP2 clathrin adaptor core with two cargo peptides in open+ conformation | |||||||||
Components |
| |||||||||
Keywords | PROTEIN TRANSPORT / ENDOCYTOSIS / TRAFFICKING / CELL MEMBRANE | |||||||||
Function / homology | Function and homology information 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 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / MHC class II antigen presentation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / VLDLR internalisation and degradation / VLDLR internalisation and degradation / MHC class II antigen presentation / Recycling pathway of L1 / AP-2 adaptor complex / regulation of vesicle size / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / maintenance of protein location in cell / Retrograde neurotrophin signalling / T cell selection / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / positive regulation of synaptic vesicle endocytosis / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / vesicle budding from membrane / MHC class II protein binding / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / MHC class II antigen presentation / protein serine/threonine kinase binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / coronary vasculature development / positive regulation of monocyte differentiation / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / negative regulation of protein localization to plasma membrane / low-density lipoprotein particle receptor binding / aorta development / regulation of T cell activation / Neutrophil degranulation / T cell receptor complex / ventricular septum development / extracellular matrix structural constituent / clathrin binding / Other interleukin signaling / 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 / EPH-ephrin mediated repulsion of cells / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / clathrin-coated pit / vesicle-mediated transport / protein tyrosine kinase binding / MHC class II antigen presentation / positive regulation of interleukin-2 production / VLDLR internalisation and degradation / phosphatidylinositol binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) Bos taurus (cattle) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å | |||||||||
Authors | Wrobel, A.G. / Owen, D.J. / McCoy, A.J. / Evans, P.R. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Dev.Cell / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qh6.cif.gz | 353.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qh6.ent.gz | 281.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/6qh6 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/6qh6 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Rattus norvegicus (Norway rat) / Gene: Ap2a2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66HM2, UniProt: P18484*PLUS |
---|---|
#2: Protein | Mass: 67091.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, ADTB2, CLAPB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63010 |
#3: Protein | Mass: 51124.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: AP2M1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZC13 |
#4: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84092 |
#7: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2s1, Ap17, Claps2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62743 |
-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.) Homo sapiens (human) |
---|---|
#6: Protein/peptide | Mass: 1314.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ACIDIC DILEUCINE INTERNALISATION SIGNAL MOTIF / Source: (synth.) Homo sapiens (human) / References: UniProt: P01730*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.9 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.252 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 5→91 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.927 / SU B: 163.978 / SU ML: 1.636 / Cross valid method: THROUGHOUT / ESU R Free: 1.382
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 5→91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|