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- PDB-9f6z: Human N-deacetylase/N-sulfotransferase 1 homodimer -

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Basic information

Entry
Database: PDB / ID: 9f6z
TitleHuman N-deacetylase/N-sulfotransferase 1 homodimer
ComponentsBifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
KeywordsBIOSYNTHETIC PROTEIN / heparan sulfate / bifunctional enzyme / Golgi / de-acetylatase & sulfotransferease
Function / homology
Function and homology information


[heparan sulfate]-glucosamine N-sulfotransferase / heparan sulfate N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparin proteoglycan biosynthetic process / embryonic neurocranium morphogenesis / embryonic viscerocranium morphogenesis / HS-GAG biosynthesis / deacetylase activity / cardiac septum development ...[heparan sulfate]-glucosamine N-sulfotransferase / heparan sulfate N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparin proteoglycan biosynthetic process / embryonic neurocranium morphogenesis / embryonic viscerocranium morphogenesis / HS-GAG biosynthesis / deacetylase activity / cardiac septum development / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / respiratory gaseous exchange by respiratory system / polysaccharide biosynthetic process / coronary vasculature development / positive regulation of smoothened signaling pathway / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / aorta development / midbrain development / forebrain development / fibroblast growth factor receptor signaling pathway / trans-Golgi network membrane / cell population proliferation / positive regulation of MAPK cascade / inflammatory response / Golgi membrane / Golgi apparatus
Similarity search - Function
Heparan sulphate-N-deacetylase / : / Heparan sulfate-N-deacetylase, deacetylase domain / Heparan sulfate-N-deacetylase, N-terminal domain / Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWild, R. / Lortat-Jacob, H. / Vallet, S.D.
Funding support France, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0006-01 France
Agence Nationale de la Recherche (ANR)ANR-21-CE29-0022 France
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
Centre National de la Recherche Scientifique (CNRS)ATIP-Avenir program France
CitationJournal: Proteoglycan Research / Year: 2023
Title: Functional and structural insights into human N-deacetylase/N-sulfotransferase activities
Authors: Vallet, S.D. / Annaval, T. / Richard, E. / Henault, J. / Le Narvor, C. / Priem, B. / Bonnaffe, D. / Vives, R.R. / Wild, R. / Lortat-Jacob, H.
History
DepositionMay 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
B: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1


Theoretical massNumber of molelcules
Total (without water)196,2292
Polymers196,2292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, 2D classes show dimers, but also monomers and tetramers, gel filtration, light scattering, Mass photometry analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 / Glucosaminyl N-deacetylase/N-sulfotransferase 1 / NDST-1 / N-heparan sulfate sulfotransferase 1 / N- ...Glucosaminyl N-deacetylase/N-sulfotransferase 1 / NDST-1 / N-heparan sulfate sulfotransferase 1 / N-HSST 1 / [Heparan sulfate]-glucosamine N-sulfotransferase 1 / HSNST 1


Mass: 98114.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein (C-terminal 8-His tag) N-terminal fusion protein (secreted alkaline phosphatase) was removed by TEV treatment, but a linker remains
Source: (gene. exp.) Homo sapiens (human) / Gene: NDST1, HSST, HSST1 / Plasmid: pTT22-SEAP / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
References: UniProt: P52848, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, [heparan sulfate]-glucosamine N-sulfotransferase
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: Homodimeric form of NDST1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pTT22-SEAP
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
18 mM2-Morpholinoethanesulfonic acidMES1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding 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: 277 K
Details: The grid was blotted for 4 s with a blot force of 0

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.4 sec. / Electron dose: 38.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3038
Image scansMovie frames/image: 44

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.3.1particle selectionblob picker
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correctionPatch CTF
9cryoSPARC3.3.1initial Euler assignmentAb-Initio
10cryoSPARC3.3.1final Euler assignmentNon-Uniform Refinement
12cryoSPARCNon-Uniform Refinement3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3554427
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 221316 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: FlexEM in CCP-EM suite
Atomic model buildingChain residue range: 65-882 / Details: dimer was calculated using AlphaFold Multimer / Source name: AlphaFold / Type: in silico model

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