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- EMDB-3589: Cryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb mi... -

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Basic information

Entry
Database: EMDB / ID: 3589
TitleCryo-EM structure of tsA201 cell alpha1B and betaI and betaIVb microtubules
SampleHuman tsA201 cell tubulin microtubules
SourceHomo sapiens / human
Map dataHEK cell tubulin microtubule cryo-EM reconstruction
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsVemu A / Atherton J
CitationMol. Biol. Cell, 2017

Mol. Biol. Cell, 2017 Yorodumi Papers
Tubulin isoform composition tunes microtubule dynamics.
Annapurna Vemu / Joseph Atherton / Jeffrey O Spector / Carolyn A Moores / Antonina Roll-Mecak

Validation ReportPDB-ID: 5n5n

SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2017 / Header (metadata) release: Jun 21, 2017 / Map release: Nov 1, 2017 / Last update: Nov 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0431
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0431
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5n5n
  • Surface level: 0.0431
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3589.map.gz (map file in CCP4 format, 12221 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
214 pix
1.22 Å/pix.
= 261.294 Å
83 pix
1.22 Å/pix.
= 101.343 Å
172 pix
1.22 Å/pix.
= 210.012 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX=Y=Z: 1.221 Å
Density
Contour Level:0.0431 (by author), 0.0431 (movie #1):
Minimum - Maximum-0.11131498 - 0.19080862
Average (Standard dev.)0.00384792 (0.016365934)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions83172214
Origin000
Limit82171213
Spacing17283214
CellA=B=C: 1 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2211.2211.221
M x/y/z17283214
origin x/y/z0.0000.0000.000
length x/y/z210.012101.343261.294
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS17283214
D min/max/mean-0.1110.1910.004

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Supplemental data

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Sample components

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Entire Human tsA201 cell tubulin microtubules

EntireName: Human tsA201 cell tubulin microtubules
Details: Microtubules formed from tsA201 cell tubulin (14pf) with bound GTP analogue GMPCPP. Tubulin was purified via TOG affinity.
Number of components: 6

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Component #1: protein, Human tsA201 cell tubulin microtubules

ProteinName: Human tsA201 cell tubulin microtubules
Details: Microtubules formed from tsA201 cell tubulin (14pf) with bound GTP analogue GMPCPP. Tubulin was purified via TOG affinity.
Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human

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Component #2: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Details: GMPCPP (GTP-analogue) bound / Recombinant expression: No
MassTheoretical: 47.735793 kDa
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: tsA201 cells

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Component #3: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Details: GTP-bound / Recombinant expression: No
MassTheoretical: 48.665027 kDa
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: tsA201 cells

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Component #4: 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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Component #5: ligand, MAGNESIUM ION

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

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Component #6: ligand, GUANOSINE-5'-TRIPHOSPHATE

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

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Experimental details

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Sample preparation

Specimen statefilament
Sample solutionSpecimen conc.: 2.5 mg/ml
Buffer solution: BRB80 with GMPCPP (80mM PIPES, 2mM MgCl2, 1mM EGTA, 1mM DTT, 1mM GMPCPP)
pH: 6.8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionSampling size: 1.221 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 13000
3D reconstructionSoftware: FREALIGN / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Gold-standard high-resolution noise substitution test employed in resolution estimation (Chen et al., 2013)

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Atomic model buiding

Output model

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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