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- EMDB-78437: Plasmodium falciparum 17-PF subpellicular microtubule associated ... -

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Basic information

Entry
Database: EMDB / ID: EMD-78437
TitlePlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (local refined map)
Map dataPlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (local refined map)
Sample
  • Organelle or cellular component: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
    • Protein or peptide: alpha tubulin 2
    • Protein or peptide: beta tubulin
    • Protein or peptide: Human Hemoglobin subunit alpha
    • Protein or peptide: Human Hemoglobin subunit beta
KeywordsPlasmodium falciparum / human hemoglobin / Tubulin / Microtubule / Microtubule-associated Protein / STRUCTURAL PROTEIN
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_78437.png

Downloads & links

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Map

FileDownload / File: emd_78437.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin (local refined map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 128 pix.
= 171.2 Å		1.34 Å/pix.
x 128 pix.
= 171.2 Å		1.34 Å/pix.
x 128 pix.
= 171.2 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: 0.008
Minimum - Maximum-0.030707574 - 0.049867377
Average (Standard dev.)0.00014227995 (±0.0021679583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 171.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_78437_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_78437_half_map_2.map
AnnotationHalf Map A
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 17-PF subpellicular microtubule associated ...

EntireName: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
Components
  • Organelle or cellular component: Plasmodium falciparum 17-PF subpellicular microtubule associated with human hemoglobin
    • Protein or peptide: alpha tubulin 2
    • Protein or peptide: beta tubulin
    • Protein or peptide: Human Hemoglobin subunit alpha
    • Protein or peptide: Human Hemoglobin subunit beta

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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: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: alpha tubulin 2

MacromoleculeName: alpha tubulin 2 / 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

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Macromolecule #2: beta tubulin

MacromoleculeName: beta tubulin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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

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Macromolecule #3: Human Hemoglobin subunit alpha

MacromoleculeName: Human 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

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Macromolecule #4: Human Hemoglobin subunit beta

MacromoleculeName: Human Hemoglobin subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.021396 KDa
SequenceString:
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATL SELHCDKLHV DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA NALAHKYH

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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
FSC plot (resolution estimation)

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