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- EMDB-3963: Cryo-EM structure of GTPgammaS-microtubule co-polymerised with do... -

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Basic information

Entry
Database: EMDB / ID: 3963
TitleCryo-EM structure of GTPgammaS-microtubule co-polymerised with doublecortin
Map dataGTPgammaS-microtubule co-polymerised with doublecortin
Sample13-PF GTPgammaS-microtubule co-polymerised with doublecortin (DCX):
Tubulin alpha-1B chain / Tubulin beta chain / (ligand) x 3
Function / homologyResolution of Sister Chromatid Cohesion / Cilium Assembly / Regulation of PLK1 Activity at G2/M Transition / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Recycling pathway of L1 / Hedgehog 'off' state / Anchoring of the basal body to the plasma membrane ...Resolution of Sister Chromatid Cohesion / Cilium Assembly / Regulation of PLK1 Activity at G2/M Transition / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Recycling pathway of L1 / Hedgehog 'off' state / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Intraflagellar transport / RHO GTPases activate IQGAPs / Hedgehog 'on' state / RHO GTPases Activate Formins / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Separation of Sister Chromatids / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Tubulin-beta mRNA autoregulation signal. / Tubulin subunits alpha, beta, and gamma signature. / Kinesins / Carboxyterminal post-translational modifications of tubulin / Tubulin / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Tubulin C-terminal domain / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding / cytoplasm / Tubulin beta chain / Tubulin alpha-1B chain
Function and homology information
Sourcesus sucrofa (pig) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsManka SW
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: The role of tubulin-tubulin lattice contacts in the mechanism of microtubule dynamic instability.
Authors: Szymon W Manka / Carolyn A Moores
Validation ReportPDB-ID: 6evy

SummaryFull reportAbout validation report
DateDeposition: Nov 3, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Jul 4, 2018 / Last update: Jul 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6evy
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3963.map.gz (map file in CCP4 format, 8285 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
1.39 Å/pix.
= 233.52 Å
134 pix
1.39 Å/pix.
= 186.26 Å
92 pix
1.39 Å/pix.
= 127.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.2783777 - 0.50152016
Average (Standard dev.)0.010249615 (0.04553814)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions13492168
Origin0.0.0.
Limit133.91.167.
Spacing92134168
CellA: 127.88 Å / B: 186.26 Å / C: 233.52 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z92134168
origin x/y/z0.0000.0000.000
length x/y/z127.880186.260233.520
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS92134168
D min/max/mean-0.2780.5020.010

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Supplemental data

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Sample components

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Entire 13-PF GTPgammaS-microtubule co-polymerised with doublecortin (DCX)

EntireName: 13-PF GTPgammaS-microtubule co-polymerised with doublecortin (DCX)
Number of components: 6

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Component #1: protein, 13-PF GTPgammaS-microtubule co-polymerised with doubleco...

ProteinName: 13-PF GTPgammaS-microtubule co-polymerised with doublecortin (DCX)
Recombinant expression: No
SourceSpecies: sus sucrofa (pig)

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Component #2: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 50.204445 kDa
SourceSpecies: Pig (pig)

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Component #3: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Pig (pig)

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Component #4: ligand, GUANOSINE-5'-TRIPHOSPHATE

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

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #6: ligand, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

LigandName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.539246 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Sample solutionpH: 6.8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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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: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 72444
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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