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- PDB-9n10: P. falciparum P-type ATPase, PfATP4 -

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Basic information

Entry
Database: PDB / ID: 9n10
TitleP. falciparum P-type ATPase, PfATP4
Components
  • Non-SERCA-type Ca2+ -transporting P-ATPase
  • PfATP4 Binding Protein (PfABP)
KeywordsMEMBRANE PROTEIN / P-type ATPase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHaile, M.T. / Zhen, J. / Ho, C.
Funding support United States, 1items
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, M.T. / Shukla, A. / Zhen, J. / Vaidya, A.B. / Ho, C.
History
DepositionJan 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-SERCA-type Ca2+ -transporting P-ATPase
B: PfATP4 Binding Protein (PfABP)


Theoretical massNumber of molelcules
Total (without water)161,8972
Polymers161,8972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Non-SERCA-type Ca2+ -transporting P-ATPase / P-type ATPase4


Mass: 140410.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum Dd2 (eukaryote) / References: UniProt: Q9U445
#2: Protein PfATP4 Binding Protein (PfABP)


Mass: 21486.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum Dd2 (eukaryote) / References: UniProt: Q8IEF9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PfATP4-PfABP / Type: COMPLEX / Details: PfATP4 co-purified with PfABP / Entity ID: all / Source: NATURAL
Source (natural)Organism: Plasmodium falciparum Dd2 (eukaryote)
Buffer solutionpH: 7.4
Details: 25 mM HEPES buffer with 10mM MgCL2, 50 mM KCL, 100 mM NaCl and 0.02% digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 447603 / Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038534
ELECTRON MICROSCOPYf_angle_d0.58611589
ELECTRON MICROSCOPYf_dihedral_angle_d5.4181144
ELECTRON MICROSCOPYf_chiral_restr0.0431348
ELECTRON MICROSCOPYf_plane_restr0.0041459

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