|Entry||Database: EMDB / ID: 7975|
|Title||Undecorated GTPgammaS microtubule|
|Map data||Undecorated GTPgammaS microtubule|
|Sample||GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds:|
Tubulin alpha-1B chain / Tubulin beta chain / (ligand) x 3
|Function / homology||Separation of Sister Chromatids / Recycling pathway of L1 / Resolution of Sister Chromatid Cohesion / 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 / Anchoring of the basal body to the plasma membrane / Tubulin-beta mRNA autoregulation signal. ...Separation of Sister Chromatids / Recycling pathway of L1 / Resolution of Sister Chromatid Cohesion / 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 / Anchoring of the basal body to the plasma membrane / Tubulin-beta mRNA autoregulation signal. / Intraflagellar transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Tubulin subunits alpha, beta, and gamma signature. / AURKA Activation by TPX2 / Tubulin C-terminal domain / 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 / 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
|Source||Sus scrofa (pig) / Pig (pig)|
|Method||helical reconstruction / cryo EM / 3.5 Å resolution|
|Authors||Zhang R / Nogales E|
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018|
Title: Separating the effects of nucleotide and EB binding on microtubule structure.
Authors: Rui Zhang / Benjamin LaFrance / Eva Nogales
Abstract: Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and ...Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.
|Validation Report||PDB-ID: 6dpw|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 9, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Jul 4, 2018 / Last update: Jul 18, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7975.map.gz (map file in CCP4 format, 536871 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.33 Å|
CCP4 map header:
+Entire GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds
|Entire||Name: GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds|
Number of components: 6
+Component #1: protein, GTPgammaS-microtubule polymerized from GMPCPP-microtubul...
|Protein||Name: GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds|
Recombinant expression: No
|Source||Species: Sus scrofa (pig)|
+Component #2: protein, Tubulin alpha-1B chain
|Protein||Name: Tubulin alpha-1B chain / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 50.204445 kDa|
|Source||Species: Pig (pig)|
+Component #3: protein, Tubulin beta chain
|Protein||Name: Tubulin beta chain / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 49.90777 kDa|
|Source||Species: Pig (pig)|
+Component #4: ligand, GUANOSINE-5'-TRIPHOSPHATE
|Ligand||Name: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 0.52318 kDa|
+Component #5: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
+Component #6: ligand, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
|Ligand||Name: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 0.539246 kDa|
|Specimen||Specimen state: helical array / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED / Delta z: 8.757 Å / Delta phi: -25.774 deg.|
|Sample solution||Specimen conc.: 5 mg/ml|
Buffer solution: Modified BRB80 buffer (80 mM PIPES, pH 6.8, 1 mM EGTA, 0.2 mM MgCl2) supplemented with 1 mM GTPgammaS, 1 mM DTT, and 0.05% Nonident P-40
|Support film||The grid was glow discharged using Solarus (Gatan Inc).|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 310 K / Humidity: 95 % / Details: Blot for 4 seconds before plunging..|
-Electron microscopy imaging
|Imaging||Microscope: FEI TITAN|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.44 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 27500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 616|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: FOURIER SPACE / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 125|
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