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- EMDB-5368: Structure of endophilin bound to a membrane tubule with a diamete... -

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Basic information

Entry
Database: EMDB / ID: EMD-5368
TitleStructure of endophilin bound to a membrane tubule with a diameter of 32nm
Map dataStructure of Endophilin bound to the bilayer
Sample
  • Sample: Structure of Endophilin bound to the bilayer
  • Protein or peptide: endophilin-A1
Biological speciesRattus norvegicus (Norway rat)
Methodhelical reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsMim C / Cui H / Gawronski-Salerno JA / Frost A / Lyman E / Voth GA / Unger VM
CitationJournal: Cell / Year: 2012
Title: Structural basis of membrane bending by the N-BAR protein endophilin.
Authors: Carsten Mim / Haosheng Cui / Joseph A Gawronski-Salerno / Adam Frost / Edward Lyman / Gregory A Voth / Vinzenz M Unger /
Abstract: Functioning as key players in cellular regulation of membrane curvature, BAR domain proteins bend bilayers and recruit interaction partners through poorly understood mechanisms. Using electron ...Functioning as key players in cellular regulation of membrane curvature, BAR domain proteins bend bilayers and recruit interaction partners through poorly understood mechanisms. Using electron cryomicroscopy, we present reconstructions of full-length endophilin and its N-terminal N-BAR domain in their membrane-bound state. Endophilin lattices expose large areas of membrane surface and are held together by promiscuous interactions between endophilin's amphipathic N-terminal helices. Coarse-grained molecular dynamics simulations reveal that endophilin lattices are highly dynamic and that the N-terminal helices are required for formation of a stable and regular scaffold. Furthermore, endophilin accommodates different curvatures through a quantized addition or removal of endophilin dimers, which in some cases causes dimerization of endophilin's SH3 domains, suggesting that the spatial presentation of SH3 domains, rather than affinity, governs the recruitment of downstream interaction partners.
History
DepositionDec 9, 2011-
Header (metadata) releaseJan 26, 2012-
Map releaseMar 26, 2012-
UpdateApr 3, 2012-
Current statusApr 3, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.48
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.48
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5368_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5368.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Endophilin bound to the bilayer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 256 pix.
= 698.88 Å		2.73 Å/pix.
x 256 pix.
= 698.88 Å		2.73 Å/pix.
x 256 pix.
= 698.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.48 / Movie #1: 1.48
Minimum - Maximum-7.28742981 - 6.35151148
Average (Standard dev.)0.00038661 (±0.99802107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 698.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z698.880698.880698.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-7.2876.3520.000

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Supplemental data

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Sample components

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Entire : Structure of Endophilin bound to the bilayer

EntireName: Structure of Endophilin bound to the bilayer
Components
  • Sample: Structure of Endophilin bound to the bilayer
  • Protein or peptide: endophilin-A1

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Supramolecule #1000: Structure of Endophilin bound to the bilayer

SupramoleculeName: Structure of Endophilin bound to the bilayer / type: sample / ID: 1000 / Oligomeric state: Dimer of endophilin bound to the bilayer / Number unique components: 1
Molecular weightExperimental: 37 MDa / Method: SDS-PAGE

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Macromolecule #1: endophilin-A1

MacromoleculeName: endophilin-A1 / type: protein_or_peptide / ID: 1 / Name.synonym: endophilin / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: rat
Molecular weightExperimental: 37 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pGEX-6 PI

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.5 / Details: 50mM potassium aspartate, 10mM Tris/HCl, 1mM EGTA
GridDetails: C-Flat, 2-2, 400nm mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 105 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot
Detailsprotein and liposomes added in solution before freezing

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJun 17, 2009
Image recordingAverage electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 30000
Sample stageSpecimen holder: eucentric, single tilt / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.27 Å
Applied symmetry - Helical parameters - Δ&Phi: 59.18 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: SPIDER,XMIPP,IHRSR
CTF correctionDetails: ACE,MATLAB

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