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- EMDB-78436: Plasmodium falciparum 18-PF subpellicular microtubule -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-78436
TitlePlasmodium falciparum 18-PF subpellicular microtubule
Map dataPlasmodium falciparum 18-PF subpellicular microtubule
Sample
  • Cell: Plasmodium falciparum 18-PF subpellicular 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
KeywordsPlasmodium falciparum / human hemoglobin / Tubulin / Microtubule / Microtubule-associated Protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / Neutrophil degranulation / microtubule-based process / microtubule cytoskeleton organization / structural constituent of cytoskeleton / mitotic cell cycle / microtubule ...Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / Neutrophil degranulation / microtubule-based process / microtubule cytoskeleton organization / structural constituent of cytoskeleton / mitotic cell cycle / microtubule / GTPase activity / GTP binding
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 (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZeng J / Zhang R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138854 United States
CitationJournal: To Be Published
Title: Human hemoglobin protects the parasite cytoskeleton during Plasmodium falciparum gametocyte development
Authors: Wang X / Zeng J / Qian P / Hasan M / Goldberg D / Zhang R
History
DepositionAug 2, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78436.png

Downloads & links

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Map

FileDownload / File: emd_78436.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum 18-PF subpellicular microtubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 512 pix.
= 684.8 Å		1.34 Å/pix.
x 512 pix.
= 684.8 Å		1.34 Å/pix.
x 512 pix.
= 684.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.2144935 - 0.50948167
Average (Standard dev.)0.0006827204 (±0.027916262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 684.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_78436_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_78436_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum 18-PF subpellicular microtubule

EntireName: Plasmodium falciparum 18-PF subpellicular microtubule
Components
  • Cell: Plasmodium falciparum 18-PF subpellicular 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: Plasmodium falciparum 18-PF subpellicular microtubule

SupramoleculeName: Plasmodium falciparum 18-PF subpellicular microtubule / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: Tubulin alpha chain

MacromoleculeName: Tubulin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 49.741211 KDa
SequenceString: MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDQ VVAGGDDAFN TFFSETGAGK HVPRCVFVDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDVCL DRVRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLAI D YGKKSKLN ...String:
MREVISIHVG QAGIQIGNAC WELFCLEHGI QPDGQMPSDQ VVAGGDDAFN TFFSETGAGK HVPRCVFVDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDVCL DRVRKLADNC TGLQGFLMFN AVGGGTGSGL GCLLLERLAI D YGKKSKLN FCSWPSPQVS TAVVEPYNSV LSTHSLLEHT DVAIMLDNEA IYDICKKNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDVTEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VSEITNSAFE PASMMAKCDP RHGKYMACCL MYR GDVVPK DVNAAVATIK TKRSIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRMDQKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GIESNDGEGE DEGYE

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: 6 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
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: 6 / 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: 6 / 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: 6 / 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: 6 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy, alkaloid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1741446
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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