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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 FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors ...Gap junction degradation / Formation of annular gap junctions / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / clathrin adaptor complex / 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 / AP-2 adaptor complex / postsynaptic endocytic zone / 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 / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / 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 / positive regulation of protein localization to membrane / Nef Mediated CD4 Down-regulation / endolysosome membrane / neurotransmitter secretion / aorta development / 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 endocytosis / positive regulation of receptor internalization / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / negative regulation of protein localization to plasma membrane / VLDLR internalisation and degradation / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / endocytic vesicle membrane / terminal bouton / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / presynapse / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / lipid binding / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / 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

#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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