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- EMDB-55773: Leishmania mexicana secreted acid phosphatase -

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Basic information

Entry
Database: EMDB / ID: EMD-55773
TitleLeishmania mexicana secreted acid phosphatase
Map data
Sample
  • Complex: Filamentous secreted acid phosphatase from Leishmania mexicana
    • Protein or peptide: Secreted acid phosphatase 1 (SAP1)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION
  • Ligand: water
KeywordsLeishmania / acid phosphatase / enzyme filaments / HYDROLASE
Function / homology: / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / phosphatase activity / Secreted acid phosphatase 1 (SAP1)
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBose P / Grossman-Haham I
Funding support Israel, 1 items
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, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55773.png

Downloads & links

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Map

FileDownload / File: emd_55773.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 384 pix.
= 341.76 Å		0.89 Å/pix.
x 384 pix.
= 341.76 Å		0.89 Å/pix.
x 384 pix.
= 341.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.8550884 - 2.5186327
Average (Standard dev.)0.00023569418 (±0.036442406)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 341.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55773_additional_1.map
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Half map: #2

Fileemd_55773_half_map_1.map
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Half map: #1

Fileemd_55773_half_map_2.map
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Sample components

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Entire : Filamentous secreted acid phosphatase from Leishmania mexicana

EntireName: Filamentous secreted acid phosphatase from Leishmania mexicana
Components
  • Complex: Filamentous secreted acid phosphatase from Leishmania mexicana
    • Protein or peptide: Secreted acid phosphatase 1 (SAP1)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Filamentous secreted acid phosphatase from Leishmania mexicana

SupramoleculeName: Filamentous secreted acid phosphatase from Leishmania mexicana
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Leishmania mexicana (eukaryote) / Location in cell: extracellular
Molecular weightTheoretical: 7.2 kDa/nm

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Macromolecule #1: Secreted acid phosphatase 1 (SAP1)

MacromoleculeName: Secreted acid phosphatase 1 (SAP1) / type: protein_or_peptide / ID: 1 / Details: The sequence provided was overexpressed / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Leishmania mexicana (eukaryote)
Molecular weightTheoretical: 62.17566 KDa
Recombinant expressionOrganism: Leishmania mexicana (eukaryote)
SequenceString: MASRLVRVLA AAMLVAAAVS VDAHFVVRMV QVVHRHGARS ALIDDNTTEI CGTLYPCGEL TGEGVEMVRA IGEFARSRYN NLSLVESPL FPSTRYNSSV VHTRSTHTQR TIQSATAFLR GLFQDDNFYP VVYSTNRTTE TLLSTDAVPS VVARSWLDNP A LHAALNPV ...String:
MASRLVRVLA AAMLVAAAVS VDAHFVVRMV QVVHRHGARS ALIDDNTTEI CGTLYPCGEL TGEGVEMVRA IGEFARSRYN NLSLVESPL FPSTRYNSSV VHTRSTHTQR TIQSATAFLR GLFQDDNFYP VVYSTNRTTE TLLSTDAVPS VVARSWLDNP A LHAALNPV IDEHLSWDAI QCAAKDAWVE GLCADYNART SCVLDMYDVA AAFEAAGRLD NATNLKAVYP GLQEVNAAWF KY VFSWNHT SKLDLTQGSA SQNLAQTVLA NINAHRLSPS YNMFQYSAHD TTVTPLAVTF GDQGETTMRP PFAVTIFVEL LQD TADASG WYVRLIRGNP VKAADGTYVF QESGIKAYCI DEAGNKYLAH TGICPLNNFR RMIDYSRPAV ADGHCTMTQT QYSN MDCPP TIADNKSVPS RCWLYRYVCP SKACPDSYIL SAVDHQCYPG SDVTNLTSSS SKSTSSSDVP SFKKPANWSP RVLSP ERGR HIAGDIIRGV TNGVTIGAGV RKHDEYSRHR QQSRMDEKTT GWRGGHVVEG LAGELEQLRA RLEHHPQGQR EPSGGC KLG LY

UniProtKB: Secreted acid phosphatase 1 (SAP1)

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 19 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: 10mM MgCL2, 100 mM NaCL, 40mM HEPES pH 7.4
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 15039 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2028299
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold prediction
Final reconstructionNumber classes used: 11 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 524666
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 100 / Avg.num./class: 20283
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9tbj:
Leishmania mexicana secreted acid phosphatase

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