+Open data
-Basic information
Entry | Database: PDB / ID: 2vgl | |||||||||
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Title | AP2 CLATHRIN ADAPTOR CORE | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / CYTOPLASMIC VESICLE / ALTERNATIVE SPLICING / ENDOCYTOSIS / LIPID-BINDING / GOLGI APPARATUS / ADAPTOR / MEMBRANE / TRANSPORT / COATED PIT / PHOSPHORYLATION | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / glutamatergic synapse / lipid binding / 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 / MIR / Resolution: 2.6 Å | |||||||||
Authors | Owen, D.J. / Collins, B.M. / McCoy, A.J. / Evans, P.R. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Molecular Architecture and Functional Model of the Endocytic Ap2 Complex Authors: Collins, B.M. / Mccoy, A.J. / Kent, H.M. / Evans, P.R. / 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 | 2vgl.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vgl.ent.gz | 283 KB | Display | PDB format |
PDBx/mmJSON format | 2vgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vgl ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vgl | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69656.297 Da / Num. of mol.: 1 / Fragment: 1-621 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)PLYSS / References: UniProt: Q66HM2, UniProt: P18484*PLUS |
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-AP-2 COMPLEX SUBUNIT ... , 3 types, 3 molecules BMS
#2: Protein | Mass: 66953.195 Da / Num. of mol.: 1 / Fragment: 1-591 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P63010 |
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#3: Protein | Mass: 49726.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)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)PLYSS / References: UniProt: P62743 |
-Non-polymers , 2 types, 13 molecules
#5: Chemical | ChemComp-IHP / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.76 % / Description: NONE | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 Details: 18% PEG, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: GE220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→67.42 Å / Num. obs: 66642 / % possible obs: 99.39 % / Observed criterion σ(I): 6 / Redundancy: 5.63 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.0515 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.16 / % possible all: 98.44 |
Reflection | *PLUS Highest resolution: 2.6 Å / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.1 |
-Processing
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Refinement | Method to determine structure: MIR / Resolution: 2.6→66.67 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / ESU R: 0.804 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 61.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→66.67 Å
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