[English] 日本語
Yorodumi
- PDB-6dpw: Undecorated GTPgammaS microtubule -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6dpw
TitleUndecorated GTPgammaS microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / cytoskeleton / GTPgammaS / seam
Function / homologySeparation of Sister Chromatids / Recruitment of mitotic centrosome proteins and complexes / Tubulin-beta mRNA autoregulation signal. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / COPI-independent Golgi-to-ER retrograde traffic / 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 NuMA to mitotic centrosomes ...Separation of Sister Chromatids / Recruitment of mitotic centrosome proteins and complexes / Tubulin-beta mRNA autoregulation signal. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / COPI-independent Golgi-to-ER retrograde traffic / 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 NuMA to mitotic centrosomes / Tubulin C-terminal domain / Recycling pathway of L1 / Hedgehog 'off' state / Cilium Assembly / Anchoring of the basal body to the plasma membrane / Intraflagellar transport / RHO GTPases activate IQGAPs / Hedgehog 'on' state / RHO GTPases Activate Formins / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, GTPase domain / COPI-dependent Golgi-to-ER retrograde traffic / Tubulin/FtsZ, C-terminal domain superfamily / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / 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 / COPI-mediated anterograde transport / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / 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 / 3.5 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7975
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7975
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)607,19430
Polyers600,67312
Non-polymers6,52018
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)52310
ΔGint (kcal/M)-250
Surface area (Å2)167350

-
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-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 6 / Formula: C10H16N5O13P3S

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: GTPgammaS-microtubule polymerized from GMPCPP-microtubule seeds
Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionDetails: 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
pH: 6.8
SpecimenConc.: 5 mg/ml
Details: GTPgammaS-microtubules were polymerized at 37 degrees for 30 minutes in the presence of GMPCPP-microtubule seeds.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was glow discharged using Solarus (Gatan Inc).
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 310 kelvins / Details: Blot for 4 seconds before plunging.

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
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: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 1.44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 616
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 1-20

-
Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
1Appionparticle selection
2Leginonimage 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: -25.774 deg. / Axial rise/subunit: 8.757 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 49145 / Algorithm: FOURIER SPACE / Number of class averages: 2 / Symmetry type: HELICAL
Atomic model buildingOverall b value: 125 / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
RefineCorrelation coeff Fo to Fc: 0.824 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 43.899 / Overall SU ML: 0.659
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: PARAMETERS FOR MASK CACLULATION
Displacement parametersB iso mean: 54.777 Å2 / Aniso B11: -5.25 Å2 / Aniso B12: -0.21 Å2 / Aniso B13: -0.2 Å2 / Aniso B22: 7.98 Å2 / Aniso B23: -1.08 Å2 / Aniso B33: -2.73 Å2
Least-squares processR factor R work: 0.39283 / R factor obs: 0.39283 / Highest resolution: 3.5 Å / Lowest resolution: 212.8 Å / Number reflection obs: 150714 / Percent reflection obs: 1
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01941742
ELECTRON MICROSCOPYr_bond_other_d0.0020.02038460
ELECTRON MICROSCOPYr_angle_refined_deg1.3471.95956718
ELECTRON MICROSCOPYr_angle_other_deg0.9413.00088482
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.5374.8115839
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.67824.2071987
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.02415.0006730
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.06215.000255
ELECTRON MICROSCOPYr_chiral_restr0.0760.2006198
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02147658
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0209828
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_it2.2245.35820598
ELECTRON MICROSCOPYr_mcbond_other2.2245.35720597
ELECTRON MICROSCOPYr_mcangle_it4.0868.02625716
ELECTRON MICROSCOPYr_mcangle_other4.0868.02725717
ELECTRON MICROSCOPYr_scbond_it2.0115.65121144
ELECTRON MICROSCOPYr_scbond_other2.0115.65321132
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.8218.32230983
ELECTRON MICROSCOPYr_long_range_B_refined8.86346.26794746
ELECTRON MICROSCOPYr_long_range_B_other8.86446.27694724
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom IDAuth asym IDEns IDNumber
1A152826
2C152826
1A252828
2E252828
1A352826
2J352826
1A452828
2K452828
1A552826
2L552826
1B652676
2D652676
1B752676
2F752676
1B852674
2G852674
1B952676
2H952676
1B1052674
2I1052674
1C1152828
2E1152828
1C1252826
2J1252826
1C1352832
2K1352832
1C1452826
2L1452826
1D1552670
2F1552670
1D1652670
2G1652670
1D1752672
2H1752672
1D1852674
2I1852674
1E1952830
2J1952830
1E2052830
2K2052830
1E2152826
2L2152826
1F2252680
2G2252680
1F2352674
2H2352674
1F2452674
2I2452674
1G2552676
2H2552676
1G2652676
2I2652676
1H2752678
2I2752678
1J2852830
2K2852830
1J2952826
2L2952826
1K3052828
2L3052828
Refine LS shellHighest resolution: 3.5 Å / R factor R work: 0.882 / Lowest resolution: 3.591 Å / Number reflection R free: 0 / Number reflection R work: 11205 / Total number of bins used: 20 / Percent reflection obs: 1

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more