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- EMDB-48801: P. falciparum P-type ATPase, PfATP4 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48801
TitleP. falciparum P-type ATPase, PfATP4
Map dataMain map used for modeling.
Sample
  • Complex: PfATP4-PfABP
    • Protein or peptide: Non-SERCA-type Ca2+ -transporting P-ATPase
    • Protein or peptide: PfATP4 Binding Protein (PfABP)
KeywordsP-type ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


P-type Na+ transporter / P-type sodium:potassium-exchanging transporter activity / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / proton transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site ...: / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Uncharacterized protein / P-type sodium-transporting ATPase4
Similarity search - Component
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_48801.png

Downloads & links

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Map

FileDownload / File: emd_48801.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map used for modeling.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.36 Å		0.82 Å/pix.
x 320 pix.
= 263.36 Å		0.82 Å/pix.
x 320 pix.
= 263.36 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: 4.8
Minimum - Maximum-51.566943999999999 - 95.252449999999996
Average (Standard dev.)0.04148491 (±1.1688069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48801_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 for main map.

Fileemd_48801_half_map_1.map
AnnotationHalf-map 1 for main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for main map.

Fileemd_48801_half_map_2.map
AnnotationHalf map 2 for main map.
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: Non-SERCA-type Ca2+ -transporting P-ATPase
    • 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: Non-SERCA-type Ca2+ -transporting P-ATPase

MacromoleculeName: Non-SERCA-type Ca2+ -transporting P-ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)
Molecular weightTheoretical: 140.410547 KDa
SequenceString: MSSQNNNKQG GQDINNKKDS DDIKPSVSKE DLINSLKNDE LNKNTTMDQN DMKKNENMNI KKNEVLNNSN NVEDGDNENS KFMNKSKEG LNNINGEKND DNNSIVKVEE SPKSIGYNYY ASESIENLCK EFGLESINTG LNSEQVKINR DKYGENFIEK D EVVPVWLI ...String:
MSSQNNNKQG GQDINNKKDS DDIKPSVSKE DLINSLKNDE LNKNTTMDQN DMKKNENMNI KKNEVLNNSN NVEDGDNENS KFMNKSKEG LNNINGEKND DNNSIVKVEE SPKSIGYNYY ASESIENLCK EFGLESINTG LNSEQVKINR DKYGENFIEK D EVVPVWLI FLSQYCSPVV LLLLVAAVAS LALNEVVEGV AIISIVTLNA CLATYMEKSS GDAIGKLAEM ASPQCTVLRN GQ KVVIPSR EVVVGDVVLI NTGDSISADL RLFDVIELKT NESLLTGESE DIKKTIVADN LSTPFATNLC FATTSVTSGS GKG IVISTG LDTQVGKIAS QLKKSSKGSK LTPLQVALNK LGGLIGLIAI IVLVVIISLA VIIKYRDPAH ADKDPTFVII IIGV GFAVS SIPEGLPMVV TITLSAGAKD MVKKNANVRK LPAVETLGCC SVICSDKTGT LTEGKMTAIN AVTICKNSSL SDENN KLTK TFDFYPTKGF EPCGGLFDSN ELTSEKKKEI VIAKNQNTSY DKVLYNYGNP SNKSVIVDKT RSLMFAAYLN SYDTTL SRD PKTLKWGIHG NMSEGPIVVA AAKVGYSFIN NPNHKSYLDN FQRLDDLEVT FNSSRKMKIT FYKLKTVNVF ENVYLDK PG KVYTHVALIK GAPDRLLDRS THLLEETSMK KVQVSWNSTI TQEERNVLIK KNLELSQKAL RVLSICIKPL TDQNIEEL K KLEDADERLK YVNYDENGGF IPMGYVASFD PPRPGVKEAI QTCREAQVKV IMITGDQKPT AVAIGKLIGL IEEKSEQVE DINSLAIECS ELHINKNPNE PILPNDQLDE FTDKILIYSR AQPEDKITIV QSLKRKGYLV AMTGDGVNDA PALKAADIGV AMGINGTEV AKGASEMILI DDNFCTVVSA IDVGRTIFSN IQKFVCFLLG TNIGEIIYLS VAIVAQMPFP LEALQILFLN L MTDGCPAV ALSREPPNDD NMKTPPRPKK QPIMTKRWWF YGILPHTIFE ALCVLLSLAF SLYICTGFYN LNGIHNLCKT VN LVDVNDA NVYHEYKYFC SSYEYRISTD YVGWVTNVSF WDPQNNEAVN FWGAAKGKVE NINPLSDIVH PELRLRMQDG CSG DLTLDE NGWCRPKDNK TSDGYNDELE GILKKGFEDV TAKGSKRGRT MAFISAVWCE MLRAYTVRSW EPFYKVFNRN MWMH LACSI SATLTFLSTC IPGITSILNT TCLLWWQYLL AIFWALLNLF LDEIVPKVIY RRKYMTIKN

UniProtKB: P-type sodium-transporting ATPase4

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Macromolecule #2: PfATP4 Binding Protein (PfABP)

MacromoleculeName: PfATP4 Binding Protein (PfABP) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)
Molecular weightTheoretical: 21.486189 KDa
SequenceString:
MGSFTEDKKE IINLEDAYKL YNFNRDNTLS ISQENDDCMP HSIILDNKSL NIFNMDSAKY QKIEYKRIFN LNSRKFTDEP NFASAISYE DVLSDSEETK KNEEENDITQ PRIHTILSFF FPFIGCLSYL INLKYPEPSL RRQYAKKALC VGSALSVIYS F ILCSLLGQ YIYQYDNKEI YGYTY

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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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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