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- EMDB-78438: Plasmodium falciparum 17-PF subpellicular microtubule associated ... -

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Basic information

Entry
Database: EMDB / ID: EMD-78438
TitlePlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
Map dataPlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (composite map)
Sample
  • Cell: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
Keywordshuman hemoglobin / Tubulin / Microtubule / Microtubule-associated Protein / STRUCTURAL PROTEIN / OXYGEN TRANSPORT-Structural Protein complex
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 / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / carbon dioxide transport / hemoglobin alpha binding ...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 / cellular oxidant detoxification / Heme assimilation / nitric oxide transport / carbon dioxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / erythrocyte development / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / oxygen carrier activity / microtubule-based process / hydrogen peroxide catabolic process / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / microtubule cytoskeleton organization / oxygen binding / Late endosomal microautophagy / platelet aggregation / positive regulation of nitric oxide biosynthetic process / structural constituent of cytoskeleton / Chaperone Mediated Autophagy / tertiary granule lumen / mitotic cell cycle / microtubule / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / inflammatory response / iron ion binding / heme binding / GTPase activity / Neutrophil degranulation / GTP binding / extracellular exosome / extracellular region / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / 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. / Globin / Globin / Globin domain profile. / 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 / Globin-like superfamily
Similarity search - Domain/homology
Hemoglobin subunit beta / Hemoglobin subunit alpha / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 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_78438.png

Downloads & links

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Map

FileDownload / File: emd_78438.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (composite map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 200 pix.
= 267.5 Å		1.34 Å/pix.
x 200 pix.
= 267.5 Å		1.34 Å/pix.
x 200 pix.
= 267.5 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: 0.1
Minimum - Maximum0.0 - 2.1220016
Average (Standard dev.)0.030980792 (±0.11367011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 267.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum 17-PF subpellicular microtubule associated ...

EntireName: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
Components
  • Cell: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Hemoglobin subunit alpha
    • Protein or peptide: Hemoglobin subunit beta
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Plasmodium falciparum 17-PF subpellicular microtubule associated ...

SupramoleculeName: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 2 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 49.66659 KDa
SequenceString: REIVHIQAGQ CGNQIGAKFW EVISDEHGID PSGTYCGDSD LQLERVDVFY NEATGGRYVP RAILMDLEPG TMDSVRAGPF GQLFRPDNF VFGQTGAGNN WAKGHYTEGA ELIDAVLDVV RKEAEGCDCL QGFQITHSLG GGTGSGMGTL LISKIREEYP D RIMETFSV ...String:
REIVHIQAGQ CGNQIGAKFW EVISDEHGID PSGTYCGDSD LQLERVDVFY NEATGGRYVP RAILMDLEPG TMDSVRAGPF GQLFRPDNF VFGQTGAGNN WAKGHYTEGA ELIDAVLDVV RKEAEGCDCL QGFQITHSLG GGTGSGMGTL LISKIREEYP D RIMETFSV FPSPKVSDTV VEPYNATLSV HQLVENADEV QVIDNEALYD ICFRTLKLTT PTYGDLNHLV SAAMSGVTCS LR FPGQLNS DLRKLAVNLI PFPRLHFFMI GFAPLTSRGS QQYRALTVPE LTQQMFDAKN MMCASDPRHG RYLTACAMFR GRM STKEVD EQMLNVQNKN SSYFVEWIPH NTKSSVCDIP PKGLKMAVTF VGNSTAIQEM FKRVSDQFTA MFRRKAFLHW YTGE GMDEM EFTEAESNMN DLVSEYQQYQ DATAEEEGEF EEEEGDVEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Hemoglobin subunit alpha

MacromoleculeName: Hemoglobin subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.28155 KDa
SequenceString:
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHA HKLRVDPVNF KLLSHCLLVT LAAHLPAEFT PAVHASLDKF LASVSTVLTS KYR

UniProtKB: Hemoglobin subunit alpha

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Macromolecule #4: Hemoglobin subunit beta

MacromoleculeName: Hemoglobin subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.890198 KDa
SequenceString:
VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG KEFTPPVQAA YQKVVAGVAN ALAHKYH

UniProtKB: Hemoglobin subunit beta

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / 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 #8: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 8 / Number of copies: 2 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

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

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Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 9 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 239215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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