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- EMDB-2018: CryoEM reconstruction of endophilin N-BAR tubes -

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Basic information

Entry
Database: EMDB / ID: EMD-2018
TitleCryoEM reconstruction of endophilin N-BAR tubes
Map dataThis is a map of an endophilin-lipid tube.
Sample
  • Sample: Endophilin N-BAR domain-lipid tube
  • Protein or peptide: endophilin BAR domain
Keywordsendocytosis / BAR / N-BAR / membrane remodeling
Biological speciesRattus norvegicus (Norway rat)
Methodhelical reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsMizuno N / Jao CC / Langen R / Steven AC
CitationJournal: 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
DepositionJan 3, 2012-
Header (metadata) releaseJan 20, 2012-
Map releaseFeb 24, 2012-
UpdateFeb 28, 2012-
Current statusFeb 28, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD2018.png

Downloads & links

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Map

FileDownload / File: emd_2018.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of an endophilin-lipid tube.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.85 Å/pix.
x 80 pix.
= 308. Å		3.85 Å/pix.
x 80 pix.
= 308. Å		3.85 Å/pix.
x 80 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.002367 - 0.01278062
Average (Standard dev.)0.00251767 (±0.00321241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.853.853.85
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z308.000308.000308.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.0020.0130.003

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Supplemental data

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Sample components

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Entire : Endophilin N-BAR domain-lipid tube

EntireName: Endophilin N-BAR domain-lipid tube
Components
  • Sample: Endophilin N-BAR domain-lipid tube
  • Protein or peptide: endophilin BAR domain

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Supramolecule #1000: Endophilin N-BAR domain-lipid tube

SupramoleculeName: Endophilin N-BAR domain-lipid tube / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: endophilin BAR domain

MacromoleculeName: endophilin BAR domain / type: protein_or_peptide / ID: 1 / Name.synonym: endophilin / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Norway Rat
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 20 mM HEPES, 100 mM NaCl
GridDetails: Quantifoil 300 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at x 100,000 magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder: Side-entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IHRSR
CTF correctionDetails: Phase flipping

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Atomic model buiding 1

Initial modelPDB ID:

2c08

RefinementSpace: REAL

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