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- PDB-6dpv: Undecorated GDP microtubule -

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Basic information

Entry
Database: PDB / ID: 6dpv
TitleUndecorated GDP microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / cytoskeleton / dynamic / seam
Function / homologySeparation 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
Specimen sourceSus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.3 Å resolution
AuthorsZhang, R. / Nogales, E.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Jun 9, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 18, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Tubulin alpha-1B chain
F: Tubulin beta chain
G: Tubulin beta chain
H: Tubulin beta chain
I: Tubulin beta chain
J: Tubulin alpha-1B chain
K: Tubulin alpha-1B chain
L: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,61730
Polyers600,67312
Non-polymers5,94418
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)49620
ΔGint (kcal/M)-270
Surface area (Å2)168620

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Components

#1: Protein/peptide
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 6 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein/peptide
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Formula: Mg / Magnesium
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Mass: 443.201 Da / Num. of mol.: 6 / Formula: C10H15N5O11P2 / Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Dynamic microtubule in GDP state / Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionDetails: BRB80 buffer (80 mM PIPES pH 6.8, 1 mM EGTA, 1 mM MgCl2) supplemented with 1 mM GTP, 1 mM DTT, and 0.05% Nonident P-40
pH: 6.8
SpecimenConc.: 3 mg/ml
Details: Microtubules were polymerized at 37 degrees for 30 minutes.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was glow discharged by Solarus (Gatan Inc).
Grid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 310 kelvins / Details: Blot for 4 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 1.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 695
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9EMANinitial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.766 deg. / Axial rise/subunit: 8.754 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 48097 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingOverall b value: 150 / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
RefineCorrelation coeff Fo to Fc: 0.743 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 37.519 / Overall SU ML: 0.596 / Overall ESU R: 1.857
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: PARAMETERS FOR MASK CACLULATION
Displacement parametersB iso mean: 32.104 Å2 / Aniso B11: -2.36 Å2 / Aniso B12: -0.37 Å2 / Aniso B13: 0.12 Å2 / Aniso B22: 5.7 Å2 / Aniso B23: 0.07 Å2 / Aniso B33: -3.34 Å2
Least-squares processR factor R work: 0.41195 / R factor obs: 0.41195 / Highest resolution: 3.3 Å / Lowest resolution: 211.48 Å / Number reflection obs: 183733 / Percent reflection obs: 1
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01941436
ELECTRON MICROSCOPYr_bond_other_d0.0020.02038172
ELECTRON MICROSCOPYr_angle_refined_deg1.3831.95856304
ELECTRON MICROSCOPYr_angle_other_deg0.9513.00087774
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.0044.8245766
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.57324.1641967
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.89615.0006652
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.05815.000257
ELECTRON MICROSCOPYr_chiral_restr0.0790.2006156
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02147376
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0209798
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.1043.18420478
ELECTRON MICROSCOPYr_mcbond_other1.1043.18420477
ELECTRON MICROSCOPYr_mcangle_it2.0594.77425566
ELECTRON MICROSCOPYr_mcangle_other2.0594.77425567
ELECTRON MICROSCOPYr_scbond_it0.8463.29820958
ELECTRON MICROSCOPYr_scbond_other0.8463.30020946
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.6404.87430719
ELECTRON MICROSCOPYr_long_range_B_refined4.91127.93594248
ELECTRON MICROSCOPYr_long_range_B_other4.91127.94094230
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Dom IDAuth asym IDEns IDNumberRms dev position
1A1519280.00
2C1519280.00
1A2519300.00
2E2519300.00
1A3518400.01
2J3518400.01
1A4518420.01
2K4518420.01
1A5519200.00
2L5519200.00
1B6518300.00
2D6518300.00
1B7518300.00
2F7518300.00
1B8518280.00
2G8518280.00
1B9518280.00
2H9518280.00
1B10518260.00
2I10518260.00
1C11519280.00
2E11519280.00
1C12518400.01
2J12518400.01
1C13518400.01
2K13518400.01
1C14519200.00
2L14519200.00
1D15518300.00
2F15518300.00
1D16518280.00
2G16518280.00
1D17518280.00
2H17518280.00
1D18518260.00
2I18518260.00
1E19518400.01
2J19518400.01
1E20518400.01
2K20518400.01
1E21519200.00
2L21519200.00
1F22518280.00
2G22518280.00
1F23518280.00
2H23518280.00
1F24518260.00
2I24518260.00
1G25518280.00
2H25518280.00
1G26518260.00
2I26518260.00
1H27518260.00
2I27518260.00
1J28519260.00
2K28519260.00
1J29518400.01
2L29518400.01
1K30518400.01
2L30518400.01
Refine LS shellHighest resolution: 3.3 Å / R factor R work: 0.749 / Lowest resolution: 3.386 Å / Number reflection R free: 0 / Number reflection R work: 13601 / Total number of bins used: 20 / Percent reflection obs: 1

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