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Open data
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Basic information
Entry | Database: PDB / ID: 2xa7 | ||||||
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Title | AP2 clathrin adaptor core in active complex with cargo peptides | ||||||
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![]() | PROTEIN TRANSPORT / PHOSPHOPROTEIN / ENDOCYTOSIS / CELL MEMBRANE / LIPID-BINDING | ||||||
Function / homology | ![]() 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 / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / 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 / Cargo recognition for clathrin-mediated endocytosis / 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 / vesicle budding from membrane / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / coronary vasculature development / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / aorta development / negative regulation of protein localization to plasma membrane / ventricular septum development / Neutrophil degranulation / low-density lipoprotein particle receptor binding / 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 / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / phosphatidylinositol binding / kidney development / intracellular protein transport / clathrin-coated endocytic vesicle membrane / terminal bouton / receptor internalization / cytoplasmic side of plasma membrane / 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 / transmembrane transporter binding / Potential therapeutics for SARS / 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 | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, L.P. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Owen, D.J. | ||||||
![]() | ![]() Title: A Large Scale Conformational Change Couples Membrane Recruitment to Cargo Binding in the Ap2 Clathrin Adaptor Complex Authors: Jackson, L.P. / Kelly, B.T. / Mccoy, A.J. / Gaffry, T. / James, L.C. / Collins, B.M. / Honing, S. / Evans, P.R. / 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 | ![]() | 719.5 KB | Display | ![]() |
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PDB format | ![]() | 602.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.3 KB | Display | ![]() |
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Full document | ![]() | 629.9 KB | Display | |
Data in XML | ![]() | 75 KB | Display | |
Data in CIF | ![]() | 100.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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 ... , 3 types, 3 molecules BMS
#2: Protein | Mass: 67091.344 Da / Num. of mol.: 1 / Fragment: BETA CHAIN, RESIDUES 1-592 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Protein/peptide / Non-polymers , 3 types, 7 molecules AP![](data/chem/img/SO4.gif)
![](data/chem/img/SO4.gif)
#1: Protein | Mass: 69656.297 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN, RESIDUES 1-621 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein/peptide | Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: HEXAPEPTIDE INTERNALISATION SIGNAL MOTIF (DYQRLN) FROM TGN38 Source: (synth.) ![]() |
#6: Chemical | ChemComp-SO4 / |
-Details
Sequence details | MYC TAG MEQKLISEED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.78 Å3/Da / Density % sol: 74.28 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.6-0.8M LISO4, 0.6-0.7M NH4SO4, 100MM NA CITRATE PH 6.5; CRYOPROTECTANT 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→64 Å / Num. obs: 66846 / % possible obs: 96.7 % / Observed criterion σ(I): -10 / Redundancy: 5.5 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.3 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 3.1→127.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 49.154 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 1.106 / ESU R Free: 0.43 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC AND LOW RESOLUTION, SO THE DETAILED CONFORMATIONS OF SIDE CHAINS IS UNRELIABLE. THE MYC TAG IN THE MU2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC AND LOW RESOLUTION, SO THE DETAILED CONFORMATIONS OF SIDE CHAINS IS UNRELIABLE. THE MYC TAG IN THE MU2 CHAIN (RESIDUES M 237-242) IS BOUND IN THE ACIDIC DILEUCINE MOTIF BINDING SITE ON THE SIGMA2 CHAIN OF A CRYSTALLOGRAPHICALLY RELATED MOLECULE, MIMICKING THE BINDING OF THIS CARGO MOTIF. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.7 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→127.88 Å
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