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- EMDB-7102: TPX2_micro decorated GMPCPP-microtubule -

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Basic information

Database: EMDB / ID: 7102
TitleTPX2_micro decorated GMPCPP-microtubule
SampleTPX2_micro decorated GMPCPP-microtubule
SourceSus scrofa / mammal / Pig / image: Sus scrofa domestica
Homo sapiens / human /
Map dataTPX2_micro decorated GMPCPP-microtubule
Methodhelical reconstruction, at 3.6 Å resolution
AuthorsZhang R / Nogales E
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural insight into TPX2-stimulated microtubule assembly.
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

Structure visualization

  • 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
3D viewer
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-9.64520.604-0.021

Supplemental data

Sample components

Entire TPX2_micro decorated GMPCPP-microtubule

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

Component #1: protein, TPX2_micro decorated GMPCPP-microtubule

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

Component #2: protein, tubulin

ProteinName: tubulin / Recombinant expression: No
SourceSpecies: Sus scrofa / mammal / Pig / image: Sus scrofa domestica

Component #3: protein, TPX2

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

Experimental details

Sample preparation

Specimen statehelical array
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

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
CameraDetector: GATAN K2 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2000

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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