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- EMDB-53571: 13 protofilament P. falciparum paclitaxel stabilised GDP microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-53571
Title13 protofilament P. falciparum paclitaxel stabilised GDP microtubule
Map dataSymmetrized 3D reconstruction of 13 protofilament Taxol stabilised microtubule
Sample
  • Organelle or cellular component: 13 protofilament paclitaxel stabilised GDP microtubule
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
KeywordsMalaria / parasite / cytoskeleton / microtubule / paclitaxel / STRUCTURAL PROTEIN
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
Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBangera M / Moores CA
Funding support United Kingdom, 1 items
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 JL / Voth G / Reber S / Moores CA
History
DepositionMay 8, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53571.png

Downloads & links

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Map

FileDownload / File: emd_53571.map.gz / Format: CCP4 / Size: 699 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetrized 3D reconstruction of 13 protofilament Taxol stabilised microtubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 568 pix.
= 606.056 Å		1.07 Å/pix.
x 568 pix.
= 606.056 Å		1.07 Å/pix.
x 568 pix.
= 606.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.065484256 - 0.16927832
Average (Standard dev.)0.0014257521 (±0.00781818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions568568568
Spacing568568568
CellA=B=C: 606.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C1 3D reconstruction of 13 protofilament Taxol stabilised microtubule

Fileemd_53571_additional_1.map
AnnotationC1 3D reconstruction of 13 protofilament Taxol stabilised microtubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_53571_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53571_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 13 protofilament paclitaxel stabilised GDP microtubule

EntireName: 13 protofilament paclitaxel stabilised GDP microtubule
Components
  • Organelle or cellular component: 13 protofilament paclitaxel stabilised GDP microtubule
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL

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Supramolecule #1: 13 protofilament paclitaxel stabilised GDP microtubule

SupramoleculeName: 13 protofilament paclitaxel stabilised GDP microtubule
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 12.5 kDa/nm

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Macromolecule #1: Tubulin alpha chain

MacromoleculeName: Tubulin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 50.34882 KDa
SequenceString: MREVISIHVG QAGIQVGNAC WELFCLEHGI QPDGQMPSDK ASRANDDAFN TFFSETGAGK HVPRCVFVDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEVIDVCL DRIRKLADNC TGLQGFLMFS AVGGGTGSGF GCLMLERLSV D YGKKSKLN ...String:
MREVISIHVG QAGIQVGNAC WELFCLEHGI QPDGQMPSDK ASRANDDAFN TFFSETGAGK HVPRCVFVDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEVIDVCL DRIRKLADNC TGLQGFLMFS AVGGGTGSGF GCLMLERLSV D YGKKSKLN FCCWPSPQVS TAVVEPYNSV LSTHSLLEHT DVAIMLDNEA IYDICRRNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDVTEFQT NLVPYPRIHF MLSSYAPVVS AEKAYHEQLS VSEITNSAFE PANMMAKCDP RHGKYMACCL MYR GDVVPK DVNAAVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRMDQKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GIESNEAEGE DEGYEADY

UniProtKB: Tubulin alpha chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 49.797781 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGTYCGDS DLQLERVDVF YNEATGGRYV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDAVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKIREEY P DRIMETFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGTYCGDS DLQLERVDVF YNEATGGRYV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDAVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKIREEY P DRIMETFS VFPSPKVSDT VVEPYNATLS VHQLVENADE VQVIDNEALY DICFRTLKLT TPTYGDLNHL VSAAMSGVTC SL RFPGQLN SDLRKLAVNL IPFPRLHFFM IGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMCASDPRH GRYLTACAMF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP HNTKSSVCDI PPKGLKMAVT FVGNSTAIQE MFKRVSDQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FEEEEGDVEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #6: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 6 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.8 / Details: BRB80 buffer - 80 mM PIPES, 2mM MgCl2, 1mM EGTA
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber 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..
DetailsTubulin 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.23 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.35 °
Applied symmetry - Helical parameters - Axial symmetry: C13 (13 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 30442
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 140038 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: An initial model obtained in ModelAngelo using the protein sequence of P. falciparum tubulin
Output model

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

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