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Open data
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Basic information
Entry | Database: PDB / ID: 6yaf | |||||||||
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Title | AP2 on a membrane containing tyrosine-based cargo peptide | |||||||||
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![]() | ENDOCYTOSIS / clathrin / clathrin adaptor / ap2 / clathrin assembly | |||||||||
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 / Retrograde transport at the Trans-Golgi-Network / 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 / trans-Golgi network transport vesicle / 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 / Golgi Associated Vesicle Biogenesis / 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 / transport vesicle / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / intracellular protein transport / kidney development / trans-Golgi network / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / endocytic vesicle membrane / terminal bouton / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / synaptic vesicle / presynapse / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / endosome / endoplasmic reticulum lumen / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / Golgi apparatus / nucleoplasm / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.1 Å | |||||||||
![]() | Kovtun, O. / Kane Dickson, V. / Kelly, B.T. / Owen, D. / Briggs, J.A.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. Authors: Oleksiy Kovtun / Veronica Kane Dickson / Bernard T Kelly / David J Owen / John A G Briggs / ![]() ![]() Abstract: Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which ...Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. Adaptor protein complex (AP2) is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here, we used cryo-electron microscopy, tomography, and subtomogram averaging to determine structures, interactions, and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5) (phosphatidylinositol 4,5-bisphosphate)-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2 appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.8 KB | Display | ![]() |
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PDB format | ![]() | 244.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 67.8 KB | Display | |
Data in CIF | ![]() | 102.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10748MC ![]() 6yaeC ![]() 6yahC ![]() 6yaiC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 70310.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 105619.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 51044.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein/peptide | Mass: 1940.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#5: Protein | Mass: 17038.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging |
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Sample preparation
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample contained AP2 and 400 nm extruded liposomes | ||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: C-flat-2/2 | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 291 K Details: The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 6500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 6500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 3.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 Details: The images were collected in movie mode at 10 frames per second |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 10 / Used frames/image: 1-10 |
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Processing
EM software |
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Image processing | Details: The images were low pass filtered according to the cumulative radiation dose. | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF correction in novaCTF with by multiplication / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100556 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
EM volume selection | Method: geometrically defined initial positions / Num. of tomograms: 112237 / Num. of volumes extracted: 585669 / Reference model: reference-free | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2XA7 Accession code: 2XA7 / Source name: PDB / Type: experimental model |