[English] 日本語
Yorodumi- PDB-4uqi: AP2 controls clathrin polymerization with a membrane-activated switch -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 4uqi | ||||||
|---|---|---|---|---|---|---|---|
| Title | AP2 controls clathrin polymerization with a membrane-activated switch | ||||||
Components | (AP-2 COMPLEX SUBUNIT ...) x 4 | ||||||
Keywords | ENDOCYTOSIS / PROTEIN TRANSPORT / LIPID BINDING | ||||||
| Function / homology | Function and homology informationLDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling ...LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / neurotransmitter secretion / endolysosome membrane / aorta development / Neutrophil degranulation / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of receptor internalization / positive regulation of endocytosis / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / terminal bouton / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
| Biological species | ![]() HOMO SAPIENS (human)![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Kelly, B.T. / Graham, S.C. / Liska, N. / Dannhauser, P.N. / Hoening, S. / Ungewickell, E.J. / Owen, D.J. | ||||||
Citation | Journal: Science / Year: 2014Title: Clathrin Adaptors. Ap2 Controls Clathrin Polymerization with a Membrane-Activated Switch. Authors: Kelly, B.T. / Graham, S.C. / Liska, N. / Dannhauser, P.N. / Honing, S. / Ungewickell, E.J. / Owen, D.J. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 4uqi.cif.gz | 702.2 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb4uqi.ent.gz | 585.7 KB | Display | PDB format |
| PDBx/mmJSON format | 4uqi.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqi ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqi | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 2vglS S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 |
| ||||||||
| Unit cell |
|
-
Components
-AP-2 COMPLEX SUBUNIT ... , 4 types, 4 molecules ABMS
| #1: Protein | Mass: 70310.062 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT TRUNK DOMAIN, RESIDUES 1-620 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
|---|---|
| #2: Protein | Mass: 73935.914 Da / Num. of mol.: 1 Fragment: BETA 2 SUBUNIT EXTENDED TRUNK DOMAIN, RESIDUES 1-651 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172 / Production host: ![]() |
| #3: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
| #4: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 5 molecules 




| #5: Chemical | ChemComp-CL / |
|---|---|
| #6: Chemical | ChemComp-IHP / |
| #7: Water | ChemComp-HOH / |
-Details
| Sequence details | CHAIN A: GLU INSERTED BETWEEN RESIDUES 271 AND 272 CHAIN M: MYC TAG INSERTED BETWEEN RESIDUES 236 AND 237 |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.37 % Description: SOLVED BY MOLECULAR REPLACEMENT FROM AN ISOMORPHOUS MODEL |
|---|---|
| Crystal grow | pH: 6.2 Details: 18% PEG1000, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6 |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9393 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 20, 2010 / Details: MIRRORS |
| Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
| Reflection | Resolution: 2.79→97.37 Å / Num. obs: 55666 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 74.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.9 |
| Reflection shell | Resolution: 2.79→2.86 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 2VGL Resolution: 2.79→97.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 33.604 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 83.089 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.79→97.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




HOMO SAPIENS (human)
X-RAY DIFFRACTION
Citation










PDBj
































