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- PDB-9r4x: 13 protofilament P. falciparum paclitaxel stabilised GDP microtubule -

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Basic information

Entry
Database: PDB / ID: 9r4x
Title13 protofilament P. falciparum paclitaxel stabilised GDP microtubule
Components
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Malaria / parasite / cytoskeleton / microtubule / paclitaxel
Function / homology
Function and homology information


Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Platelet degranulation / Aggrephagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule ...Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Platelet degranulation / Aggrephagy / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / 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 / TAXOL / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBangera, M. / Moores, C.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/Y000633/1 United Kingdom
CitationJournal: To Be Published
Title: Variations in Plasmodium tubulin determine unique microtubule architectures, mechanics and drug susceptibility.
Authors: Bangera, M. / Wu, J. / Fachet, D. / Ferreira, J.L. / Voth, G. / Reber, S. / Moores, C.A.
History
DepositionMay 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9916
Polymers100,1472
Non-polymers1,8454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Tubulin alpha chain


Mass: 50348.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q6ZLZ9
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49797.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q7KQL5

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Non-polymers , 4 types, 4 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 13 protofilament paclitaxel stabilised GDP microtubule
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 12.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 6.8 / Details: BRB80 buffer - 80 mM PIPES, 2mM MgCl2, 1mM EGTA
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Tubulin was mixed with GTP and kept in ice for 10 minutes followed by incubation in a water bath at 37 degrees for 20 minutes. Then paclitaxel was added, the sample was mixed well and ...Details: Tubulin was mixed with GTP and kept in ice for 10 minutes followed by incubation in a water bath at 37 degrees for 20 minutes. Then paclitaxel was added, the sample was mixed well and incubated in the water bath for 1 hour.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: Paclitaxel stabilized GDP microtubules were applied to a glow discharged grid, incubated for 30 seconds at room temperature following which excess sample was wicked off. This step was ...Details: Paclitaxel stabilized GDP microtubules were applied to a glow discharged grid, incubated for 30 seconds at room temperature following which excess sample was wicked off. This step was repeated again. Purified P. falciparum kinesin 8B-motor domain was immediately added to the grid, and excess sample was drawn out by pipetting. Kinesin was added again and the grid was transferred to a pre-equilibrated Vitrobot. Excess liquid was blotted off, and the grid was plunge frozen in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.75 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.1model fitting
8ISOLDE1.0b3model fitting
13RELION3.13D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -27.35 ° / Axial rise/subunit: 9.23 Å / Axial symmetry: C13
Particle selectionNum. of particles selected: 140038
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30442 / Symmetry type: HELICAL
Atomic model buildingDetails: An initial model obtained in ModelAngelo using the protein sequence of P. falciparum tubulin
Source name: Other / Type: in silico model

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