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- EMDB-7102: TPX2_micro decorated GMPCPP-microtubule -

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Basic information

Entry
Database: EMDB / ID: 7102
TitleTPX2_micro decorated GMPCPP-microtubule
Map dataTPX2_micro decorated GMPCPP-microtubule
SampleTPX2_micro decorated GMPCPP-microtubule:
tubulin / TPX2
Sourcesus scrofa (pig) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.6 Å resolution
AuthorsZhang R / Nogales E
CitationJournal: Elife / Year: 2017
Title: Structural insight into TPX2-stimulated microtubule assembly.
Authors: Rui Zhang / Johanna Roostalu / Thomas Surrey / Eva Nogales
DateDeposition: Nov 5, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7102.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.33 Å/pix.
= 680.96 Å
512 pix
1.33 Å/pix.
= 680.96 Å
512 pix
1.33 Å/pix.
= 680.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density
Contour Level:3.7 (by author), 3.7 (movie #1):
Minimum - Maximum-9.645132 - 20.603985
Average (Standard dev.)-0.021339504 (0.9093206)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin000
Limit511511511
Spacing512512512
CellA=B=C: 680.96 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z680.960680.960680.960
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-9.64520.604-0.021

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Supplemental data

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Sample components

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Entire TPX2_micro decorated GMPCPP-microtubule

EntireName: TPX2_micro decorated GMPCPP-microtubule / Number of components: 3

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Component #1: protein, TPX2_micro decorated GMPCPP-microtubule

ProteinName: TPX2_micro decorated GMPCPP-microtubule / Recombinant expression: No

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Component #2: protein, tubulin

ProteinName: tubulin / Recombinant expression: No
SourceSpecies: sus scrofa (pig)

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Component #3: protein, TPX2

ProteinName: TPX2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera aff. frugiperda 2 RZ-2014 (insect)
Strain: sf21

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 9.04 Å / Delta phi: -25.74 deg.
Sample solutionBuffer solution: BRB80 / pH: 6.8
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 95 % / Details: blot for 4 seconds before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 27.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2000

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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