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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 | ![]() protein metabolic process => GO:0019538 / 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 ...protein metabolic process => GO:0019538 / 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 / Retrograde transport at the Trans-Golgi-Network / 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 / membrane coat / vesicle budding from membrane / trans-Golgi network transport vesicle / clathrin-dependent endocytosis / MHC class II antigen presentation / membrane organization / 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 / Golgi Associated Vesicle Biogenesis / 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 / transport vesicle / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / phosphatidylinositol binding / post-translational protein modification / kidney development / Post-translational protein phosphorylation / intracellular protein transport / clathrin-coated endocytic vesicle membrane / trans-Golgi network / terminal bouton / receptor internalization / cytoplasmic side of plasma membrane / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / disordered domain specific binding / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / presynapse / cytoplasmic vesicle / protein-containing complex assembly / transmembrane transporter binding / postsynapse / Potential therapeutics for SARS / membrane => GO:0016020 / endosome / protein domain specific binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / 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
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 |