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Yorodumi- PDB-4uqi: AP2 controls clathrin polymerization with a membrane-activated switch -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uqi | ||||||
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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 information Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / 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 ...Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / 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 / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / VLDLR internalisation and degradation / MHC class II antigen presentation / Recycling pathway of L1 / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Retrograde neurotrophin signalling / 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 / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / protein serine/threonine kinase binding / coronary vasculature development / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / negative regulation of protein localization to plasma membrane / low-density lipoprotein particle receptor binding / aorta development / Neutrophil degranulation / ventricular septum development / clathrin binding / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / phosphatidylinositol binding / kidney development / clathrin-coated endocytic vesicle membrane / intracellular protein transport / terminal bouton / cytoplasmic side of plasma membrane / receptor internalization / kinase binding / endocytic vesicle membrane / disordered domain specific binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / Potential therapeutics for SARS / transmembrane transporter binding / protein domain specific binding / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
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: 2014 Title: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uqi.cif.gz | 702.2 KB | Display | PDBx/mmCIF format |
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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 |
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-Related structure data
Related structure data | 2vglS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P18484 |
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#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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P63010 |
#3: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P84092 |
#4: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P62743 |
-Non-polymers , 3 types, 5 molecules
#5: Chemical | ChemComp-CL / |
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#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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.37 % Description: SOLVED BY MOLECULAR REPLACEMENT FROM AN ISOMORPHOUS MODEL |
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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 |
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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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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.
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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
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Refinement step | Cycle: LAST / Resolution: 2.79→97.37 Å
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Refine LS restraints |
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