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- EMDB-5463: Electron cryo-microscopy of WHAMM coiled-coil domain and MTs -

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Basic information

Entry
Database: EMDB / ID: EMD-5463
TitleElectron cryo-microscopy of WHAMM coiled-coil domain and MTs
Map dataReconstruction of WHAMM coiled-coil domain with MTs
Sample
  • Sample: Helical structures of WHAMM coiled-coil and MTs
  • Protein or peptide: WHAMM coiled-coil with MTs
Keywordsactin nucleation / cryo-EM / membrane tubulation / microtubules / WHAMM
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsShen QT / Hsiue PP / Sinderlar CV / Welch MD / Wang HW / Campellone KG
CitationJournal: J Cell Biol / Year: 2012
Title: Structural insights into WHAMM-mediated cytoskeletal coordination during membrane remodeling.
Authors: Qing-Tao Shen / Peter P Hsiue / Charles V Sindelar / Matthew D Welch / Kenneth G Campellone / Hong-Wei Wang /
Abstract: The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross ...The microtubule (MT) and actin cytoskeletons drive many essential cellular processes, yet fairly little is known about how their functions are coordinated. One factor that mediates important cross talk between these two systems is WHAMM, a Golgi-associated protein that utilizes MT binding and actin nucleation activities to promote membrane tubulation during intracellular transport. Using cryoelectron microscopy and other biophysical and biochemical approaches, we unveil the underlying mechanisms for how these activities are coordinated. We find that WHAMM bound to the outer surface of MT protofilaments via a novel interaction between its central coiled-coil region and tubulin heterodimers. Upon the assembly of WHAMM onto MTs, its N-terminal membrane-binding domain was exposed at the MT periphery, where it can recruit vesicles and remodel them into tubular structures. In contrast, MT binding masked the C-terminal portion of WHAMM and prevented it from promoting actin nucleation. These results give rise to a model whereby distinct MT-bound and actin-nucleating populations of WHAMM collaborate during membrane tubulation.
History
DepositionAug 8, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5463_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5463.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of WHAMM coiled-coil domain with MTs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.8 Å/pix.
x 200 pix.
= 1560. Å		7.8 Å/pix.
x 200 pix.
= 1560. Å		7.8 Å/pix.
x 200 pix.
= 1560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.045
Minimum - Maximum-0.05469069 - 0.18331087
Average (Standard dev.)0.007509 (±0.02738204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1560.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.87.87.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1560.0001560.0001560.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0550.1830.008

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Supplemental data

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Sample components

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Entire : Helical structures of WHAMM coiled-coil and MTs

EntireName: Helical structures of WHAMM coiled-coil and MTs
Components
  • Sample: Helical structures of WHAMM coiled-coil and MTs
  • Protein or peptide: WHAMM coiled-coil with MTs

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Supramolecule #1000: Helical structures of WHAMM coiled-coil and MTs

SupramoleculeName: Helical structures of WHAMM coiled-coil and MTs / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: WHAMM coiled-coil with MTs

MacromoleculeName: WHAMM coiled-coil with MTs / type: protein_or_peptide / ID: 1 / Oligomeric state: helical / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.1 mg/mL
BufferpH: 6.8 / Details: 80mM PIPES, pH 6.8, 1mM MgCl2, 1mM EGTA, 0.5mM DTT
GridDetails: 200 mesh holy carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II / Method: load 2-3 uL and blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 110 K / Average: 100 K
DateMar 1, 2011
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: OTHER / Number real images: 110 / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 32000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
CTF correctionDetails: each particle

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