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- EMDB-8126: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with... -

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Basic information

Entry
Database: EMDB / ID: EMD-8126
TitleDimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with tubular sarcolemma model membrane
Map dataNone
Sample
  • Complex: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with sarcolemma model membrane tube
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
AuthorsDaum B / Meister A / Kuehlbrandt W
CitationJournal: J Struct Biol / Year: 2016
Title: Supramolecular organization of the human N-BAR domain in shaping the sarcolemma membrane.
Authors: Bertram Daum / Andrea Auerswald / Tobias Gruber / Gerd Hause / Jochen Balbach / Werner Kühlbrandt / Annette Meister /
Abstract: The 30kDa N-BAR domain of the human Bin1 protein is essential for the generation of skeletal muscle T-tubules. By electron cryo-microscopy and electron cryo-tomography with a direct electron ...The 30kDa N-BAR domain of the human Bin1 protein is essential for the generation of skeletal muscle T-tubules. By electron cryo-microscopy and electron cryo-tomography with a direct electron detector, we found that Bin1-N-BAR domains assemble into scaffolds of low long-range order that form flexible membrane tubules. The diameter of the tubules closely matches the curved shape of the N-BAR domain, which depends on the composition of the target membrane. These insights are fundamental to our understanding of T-tubule formation and function in human skeletal muscle.
History
DepositionMar 18, 2016-
Header (metadata) releaseApr 20, 2016-
Map releaseApr 20, 2016-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 130.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 130.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8126.png

Downloads & links

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Map

FileDownload / File: emd_8126.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.71 Å/pix.
x 100 pix.
= 770.66 Å		7.71 Å/pix.
x 100 pix.
= 770.66 Å		7.71 Å/pix.
x 100 pix.
= 770.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.7066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 130.599999999999994 / Movie #1: 130.6
Minimum - Maximum124.589979999999997 - 137.759980000000013
Average (Standard dev.)129.60517999999999 (±0.4890471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 770.66003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.70667.70667.7066
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z770.660770.660770.660
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean124.590137.760129.605

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Supplemental data

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Sample components

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Entire : Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with...

EntireName: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with sarcolemma model membrane tube
Components
  • Complex: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with sarcolemma model membrane tube

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Supramolecule #1: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with...

SupramoleculeName: Dimeric N-BAR domain of human Bin1 (Amphiphysin2) associated with sarcolemma model membrane tube
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pET14b
Molecular weightTheoretical: 60 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 10000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software: (Name: PEET, IMOD) / Number subtomograms used: 446
ExtractionNumber tomograms: 1 / Number images used: 446 / Software - Name: IMOD
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: NOT APPLICABLE

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