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- PDB-6ew0: Cryo-EM structure of GDP-microtubule co-polymerised with doubleco... -

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Basic information

Entry
Database: PDB / ID: 6ew0
TitleCryo-EM structure of GDP-microtubule co-polymerised with doublecortin and supplemented with Taxol
Components
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / microtubule / GTPase / tubulin / Taxol
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
Specimen sourceSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsManka, S.W.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 3, 2017 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 11, 2018Structure modelData collection / Database referencescitation / pdbx_database_related_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_database_related.content_type
1.2Jul 25, 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
E: Tubulin alpha-1B chain
F: Tubulin beta chain
J: Tubulin alpha-1B chain
C: Tubulin alpha-1B chain
L: Tubulin alpha-1B chain
A: Tubulin alpha-1B chain
K: Tubulin alpha-1B chain
G: Tubulin beta chain
D: Tubulin beta chain
I: Tubulin beta chain
B: Tubulin beta chain
H: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)611,74136
Polyers600,67312
Non-polymers11,06824
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)58940
ΔGint (kcal/M)-326
Surface area (Å2)173870
MethodPISA

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Components

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Protein/peptide , 2 types, 12 molecules EJCLAKFGDIBH

#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

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Non-polymers , 4 types, 24 molecules

#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
#6: Chemical
ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 6 / Formula: C47H51NO14 / Paclitaxel

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 13-PF GDP-microtubule co-polymerised with doublecortin (DCX) and supplemented with Taxol(R)
Type: COMPLEX / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 211512 / Symmetry type: POINT

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