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- EMDB-54888: The cryo-EM structure of human Tissue Nonspecific Alkaline Phosph... -

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Basic information

Entry
Database: EMDB / ID: EMD-54888
TitleThe cryo-EM structure of human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with MLS-0038949
Map data
Sample
  • Complex: Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS-0038949
    • Protein or peptide: Alkaline phosphatase, tissue-nonspecific isozyme
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: 2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide
KeywordsInhibitor / Alkaline Phosphatase / HYDROLASE
Function / homology
Function and homology information


phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development ...phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development / inhibition of non-skeletal tissue mineralization / pyrophosphatase activity / response to macrophage colony-stimulating factor / cementum mineralization / Post-translational modification: synthesis of GPI-anchored proteins / alkaline phosphatase / alkaline phosphatase activity / response to sodium phosphate / phosphate ion homeostasis / inorganic diphosphate phosphatase activity / endochondral ossification / cellular homeostasis / response to vitamin D / bone mineralization / calcium ion homeostasis / side of membrane / extracellular matrix / response to glucocorticoid / skeletal system development / response to insulin / mitochondrial membrane / mitochondrial intermembrane space / osteoblast differentiation / positive regulation of cold-induced thermogenesis / response to lipopolysaccharide / response to antibiotic / calcium ion binding / ATP hydrolysis activity / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Alkaline phosphatase, tissue-nonspecific isozyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsImam I / Coureux PD / Ballut L
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE44-0036 France
CitationJournal: To Be Published
Title: TNAP dephosphorylates phosphocholine and phosphoethanolamine and participates in triglyceride transport from the liver to the bloodstream
Authors: Drevet Mulard E / Imam I / Coureux PD / Briolay A / Bessueille L / Tarby A / Balayssac S / Narisawa S / Lecornu F / Gilard V / Violot S / Millan JL / Rautureau GJP / Ballut L / Magne D
History
DepositionAug 25, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54888.png

Downloads & links

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Map

FileDownload / File: emd_54888.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 360 pix.
= 266.4 Å		0.74 Å/pix.
x 360 pix.
= 266.4 Å		0.74 Å/pix.
x 360 pix.
= 266.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067
Minimum - Maximum-0.2632014 - 0.5391157
Average (Standard dev.)-0.00011621385 (±0.011828707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54888_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54888_half_map_2.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 : Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS...

EntireName: Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS-0038949
Components
  • Complex: Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS-0038949
    • Protein or peptide: Alkaline phosphatase, tissue-nonspecific isozyme
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: 2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide

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Supramolecule #1: Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS...

SupramoleculeName: Human Tissue Nonspecific Alkaline Phosphatase in complex with MLS-0038949
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alkaline phosphatase, tissue-nonspecific isozyme

MacromoleculeName: Alkaline phosphatase, tissue-nonspecific isozyme / type: protein_or_peptide / ID: 1
Details: on the C-terminal : TEV-protease site, FLAG-tag, His8-tag
Number of copies: 2 / Enantiomer: LEVO / EC number: alkaline phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.739297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GRALVPEKEK DPKYWRDQAQ ETLKYALELQ KLNTNVAKNV IMFLGDGMGV STVTAARILK GQLHHNPGEE TRLEMDKFPF VALSKTYNT NAQVPDSAGT ATAYLCGVKA NEGTVGVSAA TERSRCNTTQ GNEVTSILRW AKDAGKSVGI VTTTRVNHAT P SAAYAHSA ...String:
GRALVPEKEK DPKYWRDQAQ ETLKYALELQ KLNTNVAKNV IMFLGDGMGV STVTAARILK GQLHHNPGEE TRLEMDKFPF VALSKTYNT NAQVPDSAGT ATAYLCGVKA NEGTVGVSAA TERSRCNTTQ GNEVTSILRW AKDAGKSVGI VTTTRVNHAT P SAAYAHSA DRDWYSDNEM PPEALSQGCK DIAYQLMHNI RDIDVIMGGG RKYMYPKNKT DVEYESDEKA RGTRLDGLDL VD TWKSFKP RYKHSHFIWN RTELLTLDPH NVDYLLGLFE PGDMQYELNR NNVTDPSLSE MVVVAIQILR KNPKGFFLLV EGG RIDHGH HEGKAKQALH EAVEMDRAIG QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAIL YGNGP GYKVVGGERE NVSMVDYAHN NYQAQSAVPL RHETHGGEDV AVFSKGPMAH LLHGVHEQNY VPHVMAYAAC IGANL GHCA PAAAAENLYF QGDYKDDDDK HHHHHHHH

UniProtKB: Alkaline phosphatase, tissue-nonspecific isozyme

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: 2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide

MacromoleculeName: 2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide / type: ligand / ID: 9 / Number of copies: 2 / Formula: A1JNY
Molecular weightTheoretical: 344.385 Da

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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

Concentration0.07 mg/mL
BufferpH: 9
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #0 - Film thickness: 10 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was pure and monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 5000 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 194444
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1699686
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7yiv

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 465956
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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