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Yorodumi- EMDB-10752: Hexagon bounding clathrin leg in clathrin coats assembled on a me... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10752 | |||||||||
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Title | Hexagon bounding clathrin leg in clathrin coats assembled on a membrane | |||||||||
Map data | Sharpened map of hexagon bounding clathrin leg | |||||||||
Sample |
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Function / homology | Function and homology information clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / aorta development / clathrin-coated vesicle / ventricular septum development / clathrin binding / Recycling pathway of L1 / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / kidney development / clathrin-coated endocytic vesicle membrane / intracellular protein transport / cytoplasmic side of plasma membrane / endocytic vesicle membrane / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / postsynapse / Potential therapeutics for SARS / glutamatergic synapse / nucleolus / structural molecule activity / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Kovtun O / Kane Dickson V / Kelly BT / Owen D / Briggs JAG | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Sci Adv / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10752.map.gz | 9.9 MB | EMDB map data format | |
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Header (meta data) | emd-10752-v30.xml emd-10752.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10752_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_10752.png | 192.3 KB | ||
Masks | emd_10752_msk_1.map | 15.6 MB | Mask map | |
Others | emd_10752_half_map_1.map.gz emd_10752_half_map_2.map.gz | 12.9 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10752 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10752.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of hexagon bounding clathrin leg | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10752_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10752_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10752_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Clathrin/AP2 coat assembled on membrane.
Entire | Name: Clathrin/AP2 coat assembled on membrane. |
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Components |
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-Supramolecule #1: Clathrin/AP2 coat assembled on membrane.
Supramolecule | Name: Clathrin/AP2 coat assembled on membrane. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14 Details: Clathrin/AP coat was formed on the membrane containing cargo signal peptides. The AP2 adaptor lacked hinge and appendage regions in its alpha subunit. |
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Source (natural) | Organism: Sus scrofa (pig) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: C-flat-2/2 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 291 K / Instrument: LEICA EM GP Details: The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds.. | ||||||||||
Details | The sample (in vitro budding reaction) contained AP2, clathrin and 400 nm extruded liposomes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 6.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-10 / Number grids imaged: 2 / Average exposure time: 0.2 sec. / Average electron dose: 3.2 e/Å2 Details: The images were collected in movie mode at 10 frames per second |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |