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- EMDB-2157: Helical structures of WHAMM around MTs revealed by Electron cryo-... -

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Basic information

Entry
Database: EMDB / ID: EMD-2157
TitleHelical structures of WHAMM around MTs revealed by Electron cryo-microscopy
Map dataReconstruction of WHAMM with N-terminal MBP
Sample
  • Sample: WHAMM around 13-pf MTs
  • Protein or peptide: WHAMM around MTs
Keywordsactin nucleation / membrane tubulation / microtubules / WHAMM
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsShen QT / Hsiue PP / Sindelar CV / Welch MD / Campellone KG / Wang HW
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
DepositionJul 5, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.037
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.037
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2157.png

Downloads & links

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Map

FileDownload / File: emd_2157.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of WHAMM with N-terminal MBP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 200 pix.
= 740. Å		3.7 Å/pix.
x 200 pix.
= 740. Å		3.7 Å/pix.
x 200 pix.
= 740. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.037 / Movie #1: 0.037
Minimum - Maximum-0.06462937 - 0.20439057
Average (Standard dev.)0.0079912 (±0.0292616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 740.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z740.000740.000740.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0650.2040.008

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Supplemental data

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Sample components

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Entire : WHAMM around 13-pf MTs

EntireName: WHAMM around 13-pf MTs
Components
  • Sample: WHAMM around 13-pf MTs
  • Protein or peptide: WHAMM around MTs

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Supramolecule #1000: WHAMM around 13-pf MTs

SupramoleculeName: WHAMM around 13-pf MTs / type: sample / ID: 1000 / Number unique components: 117

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Macromolecule #1: WHAMM around MTs

MacromoleculeName: WHAMM around MTs / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / Strain: Hela / synonym: Human
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 6.8 / Details: 80mM PIPES pH 6.8, 1mM MgCl2, 1mM EGTA, 1mM DTT
GridDetails: 300 mesh holly carbon grid, glow discharged.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 2.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 88 K / Max: 101 K / Average: 95 K
DateNov 16, 2009
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 77 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 34000 / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.2 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.0015 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: 18.0 Å / Resolution method: OTHER / Software - Name: Spider, EMAN
CTF correctionDetails: Each particle

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Atomic model buiding 1

Initial modelPDB ID:

1jff


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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