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- EMDB-53572: 15 protofilament P. falciparum GMPCPP microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-53572
Title15 protofilament P. falciparum GMPCPP microtubule
Map dataSymmetrized 3D reconstruction of 15 protofilament GMPCPP microtubule
Sample
  • Organelle or cellular component: 15 protofilament GMPCPP microtubule
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
KeywordsMalaria / parasite / cytoskeleton / microtubule / GMPCPP / 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: 2.9 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_53572.png

Downloads & links

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Map

FileDownload / File: emd_53572.map.gz / Format: CCP4 / Size: 699 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetrized 3D reconstruction of 15 protofilament GMPCPP 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: 0.037
Minimum - Maximum-0.0823618 - 0.19585878
Average (Standard dev.)0.00071774516 (±0.008434016)
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 15 protofilament GMPCPP microtubule

Fileemd_53572_additional_1.map
AnnotationC1 3D reconstruction of 15 protofilament GMPCPP microtubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_53572_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_53572_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 15 protofilament GMPCPP microtubule

EntireName: 15 protofilament GMPCPP microtubule
Components
  • Organelle or cellular component: 15 protofilament GMPCPP microtubule
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

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Supramolecule #1: 15 protofilament GMPCPP microtubule

SupramoleculeName: 15 protofilament GMPCPP 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: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*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

Concentration0.8 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: GMPCPP microtubules were applied once or twice to a glow-discharged grid and incubated in a pre-equilibrated Vitrobot for 30 seconds at room temperature. Excess liquid was blotted off, and ...Details: GMPCPP microtubules were applied once or twice to a glow-discharged grid and incubated in a pre-equilibrated Vitrobot for 30 seconds at room temperature. Excess liquid was blotted off, and the grid was plunge frozen in liquid ethane..
DetailsTubulin was mixed with GMPCPP and kept in ice for 10 minutes followed by incubation in a water bath at 37 degrees for 2 hours.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 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: 8.17 Å
Applied symmetry - Helical parameters - Δ&Phi: -24.04 °
Applied symmetry - Helical parameters - Axial symmetry: C15 (15 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 41886
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 115668 / 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: The refined atomic model for a tubulin dimer from the 13 protofilament P. falciparum GDP-paclitaxel microtubule was used as an initial model
Output model

PDB-9r4y:
15 protofilament P. falciparum GMPCPP microtubule

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