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- EMDB-38393: Structure of prostatic acid phosphatase in human semen -

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Basic information

Entry
Database: EMDB / ID: EMD-38393
TitleStructure of prostatic acid phosphatase in human semen
Map data
Sample
  • Organelle or cellular component: structure of prostatic acid phosphatase in human semen
    • Protein or peptide: Prostatic acid phosphatase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsAcid phosphatase / CELL CYCLE
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / vesicle membrane / nucleotide metabolic process / choline binding / azurophil granule membrane / lysosome organization / phosphatase activity / purine nucleobase metabolic process / dephosphorylation / multivesicular body / protein-tyrosine-phosphatase / filopodium / protein tyrosine phosphatase activity / lipid metabolic process / apical part of cell / lysosome / molecular adaptor activity / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Histidine acid phosphatases active site signature. / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
Prostatic acid phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLiu XZ / Li JL / Deng D / Wang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: Purification, identification and Cryo-EM structure of prostatic acid phosphatase in human semen.
Authors: Xuanzhong Liu / Lin Yu / Zhili Xia / Jialu Li / Wenbo Meng / Ling Min / Fuping Li / Xiang Wang /
Abstract: Prostatic acid phosphatase (PAP) is a glycoprotein that plays a crucial role in the hydrolysis of phosphate ester present in prostatic exudates. It is a well-established indicator for prostate cancer ...Prostatic acid phosphatase (PAP) is a glycoprotein that plays a crucial role in the hydrolysis of phosphate ester present in prostatic exudates. It is a well-established indicator for prostate cancer due to its elevated serum levels in disease progression. Despite its abundance in semen, PAP's influence on male fertility has not been extensively studied. In our study, we report a significantly optimized method for purifying human endogenous PAP, achieving remarkably high efficiency and active protein recovery rate. This achievement allowed us to better analyze and understand the PAP protein. We determined the cryo-electron microscopic (Cryo-EM) structure of prostatic acid phosphatase in its physiological state for the first time. Our structural and gel filtration analysis confirmed the formation of a tight homodimer structure of human PAP. This functional homodimer displayed an elongated conformation in the cryo-EM structure compared to the previously reported crystal structure. Additionally, there was a notable 5-degree rotation in the angle between the α domain and α/β domain of each monomer. Through structural analysis, we revealed three potential glycosylation sites: Asn94, Asn220, and Asn333. These sites contained varying numbers and forms of glycosyl units, suggesting sugar moieties influence PAP function. Furthermore, we found that the active sites of PAP, His44 and Asp290, are located between the two protein domains. Overall, our study not only provide an optimized approach for PAP purification, but also offer crucial insights into its structural characteristics. These findings lay the groundwork for further investigations into the physiological function and potential therapeutic applications of this important protein.
History
DepositionDec 20, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38393.png

Downloads & links

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Map

FileDownload / File: emd_38393.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.76480734 - 1.3129894
Average (Standard dev.)0.0010774148 (±0.03546425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38393_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38393_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38393_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : structure of prostatic acid phosphatase in human semen

EntireName: structure of prostatic acid phosphatase in human semen
Components
  • Organelle or cellular component: structure of prostatic acid phosphatase in human semen
    • Protein or peptide: Prostatic acid phosphatase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: structure of prostatic acid phosphatase in human semen

SupramoleculeName: structure of prostatic acid phosphatase in human semen
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Prostatic acid phosphatase

MacromoleculeName: Prostatic acid phosphatase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acid phosphatase
Source (natural)Organism: Homo sapiens (human) / Tissue: Human seminal plasma
Molecular weightTheoretical: 40.262949 KDa
SequenceString: LAKELKFVTL VFRHGDRSPI DTFPTDPIKE SSWPQGFGQL TQLGMEQHYE LGEYIRKRYR KFLNESYKHE QVYIRSTDVD RTLMSAMTN LAALFPPEGV SIWNPILLWQ PIPVHTVPLS EDQLLYLPFR NCPRFQELES ETLKSEEFQK RLHPYKDFIA T LGKLSGLH ...String:
LAKELKFVTL VFRHGDRSPI DTFPTDPIKE SSWPQGFGQL TQLGMEQHYE LGEYIRKRYR KFLNESYKHE QVYIRSTDVD RTLMSAMTN LAALFPPEGV SIWNPILLWQ PIPVHTVPLS EDQLLYLPFR NCPRFQELES ETLKSEEFQK RLHPYKDFIA T LGKLSGLH GQDLFGIWSK VYDPLYCESV HNFTLPSWAT EDTMTKLREL SELSLLSLYG IHKQKEKSRL QGGVLVNEIL NH MKRATQI PSYKKLIMYS AHDTTVSGLQ MALDVYNGLL PPYASCHLTE LYFEKGEYFV EMYYRNETQH EPYPLMLPGC SPS CPLERF AELVGPVIPQ DWSTECMTTN S

UniProtKB: Prostatic acid phosphatase

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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: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

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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

Concentration8.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75346
FSC plot (resolution estimation)

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