+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2018 | |||||||||
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Title | CryoEM reconstruction of endophilin N-BAR tubes | |||||||||
Map data | This is a map of an endophilin-lipid tube. | |||||||||
Sample |
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Keywords | endocytosis / BAR / N-BAR / membrane remodeling | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 21.0 Å | |||||||||
Authors | Mizuno N / Jao CC / Langen R / Steven AC | |||||||||
Citation | Journal: J Biol Chem / Year: 2010 Title: Multiple modes of endophilin-mediated conversion of lipid vesicles into coated tubes: implications for synaptic endocytosis. Authors: Naoko Mizuno / Christine C Jao / Ralf Langen / Alasdair C Steven / Abstract: Endophilin A1 is a BAR (Bin/amphiphysin/Rvs) protein abundant in neural synapses that senses and induces membrane curvature, contributing to neck formation in presynaptic endocytic vesicles. To ...Endophilin A1 is a BAR (Bin/amphiphysin/Rvs) protein abundant in neural synapses that senses and induces membrane curvature, contributing to neck formation in presynaptic endocytic vesicles. To investigate its role in membrane remodeling, we used cryoelectron microscopy to characterize structural changes induced in lipid vesicles by exposure to endophilin. The vesicles convert rapidly to coated tubules whose morphology reflects the local concentration of endophilin. Their diameters and curvature resemble those of synaptic vesicles in situ. Three-dimensional reconstructions of quasicylindrical tubes revealed arrays of BAR dimers, flanked by densities that we equate with amphipathic helices whose folding and membrane insertion were attested by EPR. We also observed the compression of bulbous coated tubes into 70-A-wide cylindrical micelles, which appear to mimic the penultimate (hemi-fission) stage of endocytosis. Our findings suggest that the adaptability of endophilin-lipid interactions underlies dynamic changes of endocytic membranes. | |||||||||
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_2018.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-2018-v30.xml emd-2018.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | EMD2018.png | 99.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2018 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2018 | HTTPS FTP |
-Validation report
Summary document | emd_2018_validation.pdf.gz | 235.6 KB | Display | EMDB validaton report |
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Full document | emd_2018_full_validation.pdf.gz | 234.7 KB | Display | |
Data in XML | emd_2018_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2018 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2018 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2018.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of an endophilin-lipid tube. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Endophilin N-BAR domain-lipid tube
Entire | Name: Endophilin N-BAR domain-lipid tube |
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Components |
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-Supramolecule #1000: Endophilin N-BAR domain-lipid tube
Supramolecule | Name: Endophilin N-BAR domain-lipid tube / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: endophilin BAR domain
Macromolecule | Name: endophilin BAR domain / type: protein_or_peptide / ID: 1 / Name.synonym: endophilin / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: Norway Rat |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM HEPES, 100 mM NaCl |
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Grid | Details: Quantifoil 300 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at x 100,000 magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 66000 |
Sample stage | Specimen holder: Side-entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IHRSR |
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CTF correction | Details: Phase flipping |
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL |