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- EMDB-1787: Asymmetric reconstruction of doublecortin-stabilised microtubules... -

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Basic information

Entry
Database: EMDB / ID: 1787
TitleAsymmetric reconstruction of doublecortin-stabilised microtubules decorated with kinesin motor domain
KeywordsTubulin / MAP / microtubule / stabilisation / doublecortin / kinesin
SampleMicrotubules co-polymerised with doublecortin and bound with kinesin motor domain
SourceBos taurus / mammal / Bovine / ウシ /
Homo sapiens / human
Rattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /
Map dataThis is a C1 reconstruction of doublecortin-stabilised microtubule decorated with kinesin motor domain
Methodsingle particle reconstruction, at 13.5 Å resolution
AuthorsFourniol FJ / Sindelar CV / Amigues B / Clare D / Thomas G / Perderiset M / Francis F / Houdusse A / Moores CA
CitationJ. Cell Biol., 2010, 191, 463-470

J. Cell Biol., 2010, 191, 463-470 Yorodumi Papers
Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution.
Franck J Fourniol / Charles V Sindelar / Béatrice Amigues / Daniel K Clare / Geraint Thomas / Mylène Perderiset / Fiona Francis / Anne Houdusse / Carolyn A Moores

DateDeposition: Sep 15, 2010 / Header (metadata) release: Sep 24, 2010 / Map release: Oct 29, 2010 / Last update: Sep 19, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1787.map.gz (map file in CCP4 format, 39367 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
216 pix
2.8 Å/pix.
= 604.8 Å
216 pix
2.8 Å/pix.
= 604.8 Å
216 pix
2.8 Å/pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-3.84556389 - 7.45892239
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions216216216
Origin000
Limit215215215
Spacing216216216
CellA=B=C: 604.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-3.8467.459-0.000

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Supplemental data

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Sample components

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Entire Microtubules co-polymerised with doublecortin and bound with kine...

EntireName: Microtubules co-polymerised with doublecortin and bound with kinesin motor domain
Number of components: 3 / Oligomeric State: 13-protofilament microtubule

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Component #1: protein, Alpha-beta tubulin dimer

ProteinName: Alpha-beta tubulin dimer / a.k.a: Tubulin dimer / Oligomeric Details: Heterodimer / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / Bovine / ウシ /
Source (natural)Location in cell: Cytoplasm / Organ or tissue: Brain

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Component #2: protein, Doublecortin

ProteinName: Doublecortin / a.k.a: DCX / Oligomeric Details: Monomer / Recombinant expression: Yes
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Vector: pFastBac
Source (natural)Location in cell: Cytoplasm

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Component #3: protein, Kinesin motor domain

ProteinName: Kinesin motor domain / a.k.a: Kinesin head / Oligomeric Details: Monomer / Recombinant expression: Yes
SourceSpecies: Rattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Location in cell: Cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 80mM Pipes, 1mM EGTA, 3mM MgCl2, 1mM TCEP, 0.5mM GTP
pH: 6.8
Support film300 mesh lacey carbon grids
Stainingcryo-EM
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: Chamber at 37 degrees C, blot 2s / Details: Vitrification instrument: Vitrobot (FEI)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 760 - 2900 nm
Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 63 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / Details: Images were binned with a factor of 2

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Image processing

ProcessingMethod: single particle reconstruction
3D reconstructionAlgorithm: Custom scripts, projection matching / Software: SPIDER, FREALIGN / CTF correction: FREALIGN
Details: C1 map calculated from approximately 13,000 one-dimer-long microtubule segments
Resolution: 13.5 Å / Resolution method: FSC 0.5

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