[English] 日本語
Yorodumi
- PDB-6dpu: Undecorated GMPCPP microtubule -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6dpu
TitleUndecorated GMPCPP microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / cytoskeleton / GMPCPP / 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 / 3.1 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-7973
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7973
  • 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)607,23136
Polyers600,67312
Non-polymers6,55824
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)50380
ΔGint (kcal/M)-322
Surface area (Å2)168010

-
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.: 12 / Formula: Mg / Magnesium
#5: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 6 / Formula: C11H18N5O13P3 / Comment: GMP-CPP (energy-carrying molecule analogue) *YM

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: microtubule stabilized by GMPCPP / 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 GMPCPP, 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: Glow discharge was performed with Pelco EasiGlow device.
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: 298 kelvins / Details: Blot for 4 seconds before plunging.

-
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: 105000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2700 nm / Cs: 0.01 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 1.33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1176
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Sph aberration corrector: Microscope has a Cs corrector.
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

+
Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
1Appionparticle selection
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9REFMACmodel refinement
10EMANinitial Euler assignment
11FREALIGNfinal Euler assignment
13FREALIGN3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.75 deg. / Axial rise/subunit: 8.99 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 110127 / 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: 0.768 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 32.588 / Overall SU ML: 0.54 / Overall ESU R: 0.978
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: PARAMETERS FOR MASK CACLULATION
Displacement parametersB iso mean: 29.477 Å2 / Aniso B11: -3.04 Å2 / Aniso B12: -0.23 Å2 / Aniso B13: -0.3 Å2 / Aniso B22: 8.45 Å2 / Aniso B23: -0.38 Å2 / Aniso B33: -5.41 Å2
Least-squares processR factor R work: 0.41337 / R factor obs: 0.41337 / Highest resolution: 3.1 Å / Lowest resolution: 214.82 Å / Number reflection obs: 232359 / Percent reflection obs: 1
Number of atoms included #1Total: 40650
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01941574
ELECTRON MICROSCOPYr_bond_other_d0.0020.02038316
ELECTRON MICROSCOPYr_angle_refined_deg1.4451.95956490
ELECTRON MICROSCOPYr_angle_other_deg0.9723.00088134
ELECTRON MICROSCOPYr_dihedral_angle_1_deg12.2044.8365813
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.06824.2131956
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.03315.0006693
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.90115.000251
ELECTRON MICROSCOPYr_chiral_restr0.0820.2006174
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02147472
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0209792
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_it0.9472.92820550
ELECTRON MICROSCOPYr_mcbond_other0.9472.92820549
ELECTRON MICROSCOPYr_mcangle_it1.7714.38825656
ELECTRON MICROSCOPYr_mcangle_other1.7714.38825657
ELECTRON MICROSCOPYr_scbond_it0.6953.04121024
ELECTRON MICROSCOPYr_scbond_other0.6953.04221012
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.3604.49530815
ELECTRON MICROSCOPYr_long_range_B_refined4.30226.01095315
ELECTRON MICROSCOPYr_long_range_B_other4.30226.01595297
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
1A152726
2C152726
1A252728
2E252728
1A352718
2J352718
1A452720
2K452720
1A552718
2L552718
1B652638
2D652638
1B752638
2F752638
1B852636
2G852636
1B952634
2H952634
1B1052632
2I1052632
1C1152728
2E1152728
1C1252718
2J1252718
1C1352724
2K1352724
1C1452722
2L1452722
1D1552644
2F1552644
1D1652642
2G1652642
1D1752640
2H1752640
1D1852640
2I1852640
1E1952724
2J1952724
1E2052722
2K2052722
1E2152720
2L2152720
1F2252648
2G2252648
1F2352642
2H2352642
1F2452640
2I2452640
1G2552642
2H2552642
1G2652640
2I2652640
1H2752640
2I2752640
1J2852720
2K2852720
1J2952722
2L2952722
1K3052724
2L3052724
Refine LS shellHighest resolution: 3.1 Å / R factor R work: 0.736 / Lowest resolution: 3.18 Å / Number reflection R free: 0 / Number reflection R work: 17224 / 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