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- PDB-6e88: Cryo-EM structure of C. elegans GDP-microtubule -

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Basic information

Entry
Database: PDB / ID: 6.0E+88
TitleCryo-EM structure of C. elegans GDP-microtubule
Components
  • Tubulin alpha-2 chain
  • Tubulin beta-2 chain
KeywordsSTRUCTURAL PROTEIN / Cytoskeletal protein
Function / homology
Function and homology information


COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / Neutrophil degranulation / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex ...COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / Neutrophil degranulation / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex / establishment of mitotic spindle orientation / regulation of cytokinesis / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / protein localization / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-2 chain / Tubulin beta-2 chain
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChaaban, S. / Jariwala, S. / Chieh-Ting, H. / Redemann, S. / Kollman, J. / Muller-Reichert, T. / Sept, D. / Bui, K.H. / Brouhard, G.J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-137055 Canada
Canadian Institutes of Health Research (CIHR)PJT-148702 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)03791 Canada
CitationJournal: Dev Cell / Year: 2018
Title: The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth.
Authors: Sami Chaaban / Shashank Jariwala / Chieh-Ting Hsu / Stefanie Redemann / Justin M Kollman / Thomas Müller-Reichert / David Sept / Khanh Huy Bui / Gary J Brouhard /
Abstract: The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and ...The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first / _entity.formula_weight
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Tubulin alpha-2 chain
B: Tubulin beta-2 chain
C: Tubulin alpha-2 chain
D: Tubulin beta-2 chain
H: Tubulin alpha-2 chain
J: Tubulin beta-2 chain
L: Tubulin alpha-2 chain
N: Tubulin beta-2 chain
I: Tubulin alpha-2 chain
K: Tubulin beta-2 chain
M: Tubulin alpha-2 chain
O: Tubulin beta-2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)583,66824
Polymers577,87012
Non-polymers5,79812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area50540 Å2
ΔGint-209 kcal/mol
Surface area186980 Å2

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Components

#1: Protein
Tubulin alpha-2 chain


Mass: 48467.609 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / Strain: N2 / References: UniProt: P34690
#2: Protein
Tubulin beta-2 chain / Beta-2-tubulin


Mass: 47843.988 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / Strain: N2 / References: UniProt: P52275
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: microtubule / Type: ORGANELLE OR CELLULAR COMPONENT
Details: C. elegans microtubules polymerized in the presence of GTP
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 165 kDa/nm / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2
Buffer solutionpH: 6.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 29.33 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16574 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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