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- EMDB-7101: TPX2_mini decorated GMPCPP-microtubule -

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Basic information

Entry
Database: EMDB / ID: 7101
TitleTPX2_mini decorated GMPCPP-microtubule
SampleTPX2_mini decorated GMPCPP-microtubule
SourceSus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Homo sapiens / human
Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Map dataTPX2_mini decorated GMPCPP- microtubule
Methodhelical reconstruction, at 3.3 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

Validation ReportPDB-ID: 6bjc

SummaryFull reportAbout validation report
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 colored by cylindrical radius
  • Surface level: 3.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with section colored by density value
  • Surface level: 3.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bjc
  • Surface level: 3.7
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6bjc
  • Imaged by Jmol
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_7101.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

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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 package.

Voxel sizeX=Y=Z: 1.33 Å
Density
Contour Level:3.7 (by author), 3.7 (movie #1):
Minimum - Maximum-12.16531 - 25.345736
Average (Standard dev.)-0.016123138 (0.93212706)
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-12.16525.346-0.016

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Supplemental data

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Sample components

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Entire TPX2_mini decorated GMPCPP-microtubule

EntireName: TPX2_mini decorated GMPCPP-microtubule / Number of components: 9

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Component #1: protein, TPX2_mini decorated GMPCPP-microtubule

ProteinName: TPX2_mini decorated GMPCPP-microtubule / Recombinant expression: No

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Component #2: protein, Tubulin

ProteinName: Tubulin / Recombinant expression: No
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #3: protein, Targeting protein for Xklp2

ProteinName: Targeting protein for Xklp2 / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Spodoptera aff. frugiperda 2 rz-2014 / arthropod
Strain: sf21

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Component #4: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Recombinant expression: No
MassTheoretical: 50.204445 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #5: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Component #6: protein, Targeting protein for Xklp2

ProteinName: Targeting protein for Xklp2 / Recombinant expression: No
MassTheoretical: 85.811328 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #7: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #9: ligand, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

LigandName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.521208 kDa

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 9.03 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 27.6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 0.01 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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