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- PDB-9tbj: Leishmania mexicana secreted acid phosphatase -

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Basic information

Entry
Database: PDB / ID: 9tbj
TitleLeishmania mexicana secreted acid phosphatase
ComponentsSecreted acid phosphatase 1 (SAP1)
KeywordsHYDROLASE / Leishmania / acid phosphatase / enzyme filaments
Function / homology: / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / phosphatase activity / PHOSPHATE ION / Secreted acid phosphatase 1 (SAP1)
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBose, P. / Grossman-Haham, I.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1691/23 Israel
CitationJournal: Protein Sci / Year: 2026
Title: Structural basis of secreted acid phosphatase polymerization in the Leishmania parasite.
Authors: Priyanka Bose / Irit Dahan / Alexander Upcher / Ran Zalk / Iris Grossman-Haham /
Abstract: Enzymes that assemble into filaments typically transition between protomeric and polymeric states in response to cellular conditions. In contrast, the secreted acid phosphatase (SAP) of Leishmania, ...Enzymes that assemble into filaments typically transition between protomeric and polymeric states in response to cellular conditions. In contrast, the secreted acid phosphatase (SAP) of Leishmania, one of the most abundant extracellular glycoproteins produced by the parasite and regarded as a major virulence factor in the neglected tropical disease leishmaniasis, exhibits fundamentally different behavior. Depending on the species, SAP forms either highly stable extracellular filaments or remains exclusively as globular particles, with no evidence of reversible interconversion. This binary assembly pattern is particularly intriguing given that SAP orthologs that differ in their ability to polymerize share a high degree of sequence conservation, leaving the molecular determinants of filament formation unknown. Here, we report the cryo-EM structure of filamentous Leishmania mexicana SAP to a global resolution of 3.0 Å. The structure resolves the multilevel organization of the enzyme, from individual catalytic phosphatase domains and their unique substrate-binding pockets to the formation of homodimeric protomers, the decoration with N-linked glycans, and the supramolecular organization into filaments. At the core of the polymerization interface, we identified a unique β-hairpin motif that has not been observed in any other phosphatase or enzyme filament, which provides exceptional filament stability. By integrating structural data with comparative sequence analysis and machine-learning-based structure predictions, we define the molecular basis for the species-specific assembly behaviors observed across Leishmania SAPs. This work establishes the principles governing SAP filament formation and provides a framework for understanding its evolution, enzymatic function, and potential applications.
History
DepositionNov 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted acid phosphatase 1 (SAP1)
B: Secreted acid phosphatase 1 (SAP1)
C: Secreted acid phosphatase 1 (SAP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,28321
Polymers186,5273
Non-polymers5,75618
Water34219
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

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Protein , 1 types, 3 molecules ABC

#1: Protein Secreted acid phosphatase 1 (SAP1)


Mass: 62175.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The sequence provided was overexpressed / Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: lmsap1 / Plasmid: pX / Details (production host): pX-H-SBP-ORF-H / Production host: Leishmania mexicana (eukaryote) / References: UniProt: Q25332

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Sugars , 3 types, 15 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 22 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Filamentous secreted acid phosphatase from Leishmania mexicana
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.2 kDa/nm / Experimental value: NO
Source (natural)Organism: Leishmania mexicana (eukaryote) / Cellular location: extracellular
Source (recombinant)Organism: Leishmania mexicana (eukaryote) / Plasmid: pX
Buffer solutionpH: 7.4 / Details: 10mM MgCL2, 100 mM NaCL, 40mM HEPES pH 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 15039
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_4985 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2028299
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 524666 / Num. of class averages: 11 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003310485
ELECTRON MICROSCOPYf_angle_d0.62114326
ELECTRON MICROSCOPYf_chiral_restr0.04391680
ELECTRON MICROSCOPYf_plane_restr0.00621828
ELECTRON MICROSCOPYf_dihedral_angle_d4.15271396

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