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- EMDB-2007: Structural Basis of Membrane Bending by the N-BAR Protein Endophilin -

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Basic information

Entry
Database: EMDB / ID: EMD-2007
TitleStructural Basis of Membrane Bending by the N-BAR Protein Endophilin
Map dataThis a reconstruction of the endophilin A1 N-BAR domain bound to a membrane tubule with a diameter of 25 nm.
Sample
  • Sample: N-BAR domain (1-247) of rat endophilinA1
  • Protein or peptide: rat endophilinA1 N-BAR domain
Biological speciesRattus norvegicus (Norway rat)
Methodhelical reconstruction / cryo EM / Resolution: 16.0 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) releaseApr 27, 2012-
Map releaseApr 27, 2012-
UpdateApr 27, 2012-
Current statusApr 27, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.94
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.94
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2007.tif

Downloads & links

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Map

FileDownload / File: emd_2007.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis a reconstruction of the endophilin A1 N-BAR domain bound to a membrane tubule with a diameter of 25 nm.
Voxel sizeX=Y=Z: 2.73 Å
Density
Contour LevelBy AUTHOR: 1.94 / Movie #1: 1.94
Minimum - Maximum-5.26045322 - 5.55220652
Average (Standard dev.)0.00054419 (±0.99662787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 491.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z491.400491.400491.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-5.2605.5520.001

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Supplemental data

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Sample components

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Entire : N-BAR domain (1-247) of rat endophilinA1

EntireName: N-BAR domain (1-247) of rat endophilinA1
Components
  • Sample: N-BAR domain (1-247) of rat endophilinA1
  • Protein or peptide: rat endophilinA1 N-BAR domain

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Supramolecule #1000: N-BAR domain (1-247) of rat endophilinA1

SupramoleculeName: N-BAR domain (1-247) of rat endophilinA1 / type: sample / ID: 1000
Oligomeric state: Dimer of the N-BAR domain of endophilin binds to bilayer
Number unique components: 1
Molecular weightExperimental: 25 MDa

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Macromolecule #1: rat endophilinA1 N-BAR domain

MacromoleculeName: rat endophilinA1 N-BAR domain / type: protein_or_peptide / ID: 1 / Name.synonym: N-BAR domain / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Norway rat / Location in cell: Plasma membrane
Molecular weightExperimental: 25 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 K-Aspartate, 10mM Tris, 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 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0014 µm / Nominal magnification: 30000
Sample stageSpecimen holder: eucentric, single tilt / Specimen holder model: GATAN LIQUID NITROGEN
DetailsLow Dose Imaging
Image recordingAverage electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: ACE,MATLAB
Final reconstructionApplied symmetry - Helical parameters - Δz: 25.13 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.57 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: SPIDER,XMIPP,IHRSR

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