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- EMDB-48800: P. falciparum P-type ATPase, PfATP4 re-centered in the P-domain -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48800
TitleP. falciparum P-type ATPase, PfATP4 re-centered in the P-domain
Map dataRe-centered map used for modeling P- and N- domains
Sample
  • Complex: PfATP4-PfABP
    • Protein or peptide: P-type sodium-transporting ATPase4
    • Protein or peptide: PfATP4 binding protein (PfABP)
KeywordsP-type ATPase / MEMBRANE PROTEIN
Function / homologymembrane / Uncharacterized protein
Function and homology information
Biological speciesPlasmodium falciparum Dd2 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHaile MT / Zhen J / Ho C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD029613 United States
CitationJournal: Nat Commun / Year: 2025
Title: Endogenous structure of antimalarial target PfATP4 reveals an apicomplexan-specific P-type ATPase modulator
Authors: Haile MT / Shukla A / Zhen J / Vaidya AB / Ho C
History
DepositionJan 24, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48800.png

Downloads & links

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Map

FileDownload / File: emd_48800.map.gz / Format: CCP4 / Size: 187 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRe-centered map used for modeling P- and N- domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 366 pix.
= 301.218 Å		0.82 Å/pix.
x 366 pix.
= 301.218 Å		0.82 Å/pix.
x 366 pix.
= 301.218 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.308885 - 0.46120447
Average (Standard dev.)0.00022752974 (±0.0058829216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions366366366
Spacing366366366
CellA=B=C: 301.21802 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48800_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_48800_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_48800_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 : PfATP4-PfABP

EntireName: PfATP4-PfABP
Components
  • Complex: PfATP4-PfABP
    • Protein or peptide: P-type sodium-transporting ATPase4
    • Protein or peptide: PfATP4 binding protein (PfABP)

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Supramolecule #1: PfATP4-PfABP

SupramoleculeName: PfATP4-PfABP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PfATP4 co-purified with PfABP
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)

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Macromolecule #1: P-type sodium-transporting ATPase4

MacromoleculeName: P-type sodium-transporting ATPase4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: P-type Na+ transporter
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)
SequenceString: MSSQNNNKQG GQDINNKKDS DDIKPSVSKE DLINSLKNDE LNKNTTMDQN DMKKNENMNI KKNEVLNNSN NVEDGDNENS KFMNKSKEGL NNINGEKNDD NNSIVKVEES PKSIGYNYYA SESIENLCKE FGLESINTGL NSEQVKINRD KYGENFIEKD EVVPVWLIFL ...String:
MSSQNNNKQG GQDINNKKDS DDIKPSVSKE DLINSLKNDE LNKNTTMDQN DMKKNENMNI KKNEVLNNSN NVEDGDNENS KFMNKSKEGL NNINGEKNDD NNSIVKVEES PKSIGYNYYA SESIENLCKE FGLESINTGL NSEQVKINRD KYGENFIEKD EVVPVWLIFL SQYCSPVVLL LLVAAVASLA LNEVVEGVAI ISIVTLNACL ATYMEKSSGD AIGKLAEMAS PQCTVLRNGQ KVVIPSREVV VGDVVLINTG DSISADLRLF DVIELKTNES LLTGESEDIK KTIVADNLST PFATNLCFAT TSVTSGSGKG IVISTGLDTQ VGKIASQLKK SSKGSKLTPL QVALNKLGGL IGLIAIIVLV VIISLAVIIK YRDPAHADKD PTFVIIIIGV GFAVSSIPEG LPMVVTITLS AGAKDMVKKN ANVRKLPAVE TLGCCSVICS DKTGTLTEGK MTAINAVTIC KNSSLSDENN KLTKTFDFYP TKGFEPCGGL FDSNELTSEK KKEIVIAKNQ NTSYDKVLYN YGNPSNKSVI VDKTRSLMFA AYLNSYDTTL SRDPKTLKWG IHGNMSEGPI VVAAAKVGYS FINNPNHKSY LDNFQRLDDL EVTFNSSRKM KITFYKLKTV NVFENVYLDK PGKVYTHVAL IKGAPDRLLD RSTHLLEETS MKKVQVSWNS TITQEERNVL IKKNLELSQK ALRVLSICIK PLTDQNIEEL KKLEDADERL KYVNYDENGG FIPMGYVASF DPPRPGVKEA IQTCREAQVK VIMITGDQKP TAVAIGKLIG LIEEKSEQVE DINSLAIECS ELHINKNPNE PILPNDQLDE FTDKILIYSR AQPEDKITIV QSLKRKGYLV AMTGDGVNDA PALKAADIGV AMGINGTEVA KGASEMILID DNFCTVVSAI DVGRTIFSNI QKFVCFLLGT NIGEIIYLSV AIVAQMPFPL EALQILFLNL MTDGCPAVAL SREPPNDDNM KTPPRPKKQP IMTKRWWFYG ILPHTIFEAL CVLLSLAFSL YICTGFYNLN GIHNLCKTVN LVDVNDANVY HEYKYFCSSY EYRISTDYVG WVTNVSFWDP QNNEAVNFWG AAKGKVENIN PLSDIVHPEL RLRMQDGCSG DLTLDENGWC RPKDNKTSDG YNDELEGILK KGFEDVTAKG SKRGRTMAFI SAVWCEMLRA YTVRSWEPFY KVFNRNMWMH LACSISATLT FLSTCIPGIT SILNTTCLLW WQYLLAIFWA LLNLFLDEIV PKVIYRRKYM TIKN

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Macromolecule #2: PfATP4 binding protein (PfABP)

MacromoleculeName: PfATP4 binding protein (PfABP) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)
SequenceString:
MGSFTEDKKE IINLEDAYKL YNFNRDNTLS ISQENDDCMP HSIILDNKSL NIFNMDSAKY QKIEYKRIFN LNSRKFTDEP NFASAISYED VLSDSEETKK NEEENDITQP RIHTILSFFF PFIGCLSYLI NLKYPEPSLR RQYAKKALCV GSALSVIYSF ILCSLLGQYI YQYDNKEIYG YTY

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 25 mM HEPES buffer with 10mM MgCL2, 50 mM KCL, 100 mM NaCl and 0.02% digitonin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 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: 1.5 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 447603
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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