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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: Nat Commun / Year: 2026
Title: Adaptations in Plasmodium tubulin determine distinct microtubule architectures, mechanics and drug susceptibility.
Authors: Mamata Bangera / Jiangbo Wu / Daniel Beckett / Dominik Fachet / Josie L Ferreira / Gregory A Voth / Simone Reber / Carolyn A Moores /
Abstract: Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by ...Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by which microtubule architecture varies through the life cycle of the malaria-causing parasite Plasmodium are not understood and provide a valuable framework for exploring how intrinsic properties of tubulin contribute to architectural variety. Using parasite-purified tubulin, we determine P. falciparum microtubule structures by cryo-electron microscopy. Parasite-specific sequences change the tubulin dimer structure, suggesting how drug susceptibility and polymer properties are modified. Within the P. falciparum microtubule, lateral contacts are smaller but stronger, and the lattice is stiffer than in brain microtubules. Non-canonical microtubule architectures found in parasites are highly similar to those observed in vitro, validating the physiological relevance of these properties. Our findings show how evolutionary adaptation of tubulin modulates the material properties of the microtubule cytoskeleton.
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
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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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