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- EMDB-17349: Human N-deacetylase/N-sulfotransferase 1 homodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-17349
TitleHuman N-deacetylase/N-sulfotransferase 1 homodimer
Map dataEM map of human NDST1 homodimer
Sample
  • Complex: NDST1 homodimer
    • Protein or peptide: N-deacetylase/N-sulfotransferase 1
Keywordsheparan sulfate / bifunctional enzyme / Golgi / de-acetylatase & sulfotransferease / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


[heparan sulfate]-glucosamine N-sulfotransferase / [heparan sulfate]-glucosamine N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin biosynthetic process / embryonic viscerocranium morphogenesis / embryonic neurocranium morphogenesis / HS-GAG biosynthesis ...[heparan sulfate]-glucosamine N-sulfotransferase / [heparan sulfate]-glucosamine N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / heparin biosynthetic process / embryonic viscerocranium morphogenesis / embryonic neurocranium morphogenesis / HS-GAG biosynthesis / deacetylase activity / cardiac septum development / respiratory gaseous exchange by respiratory system / coronary vasculature development / positive regulation of smoothened signaling pathway / aorta development / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / midbrain development / fibroblast growth factor receptor signaling pathway / forebrain development / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsVallet SD / Lortat-Jacob H / Wild R
Funding support France, 4 items
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 Res / Year: 2023
Title: Functional and structural insights into human N-deacetylase/N-sulfotransferase activities
Authors: Vallet SD / Annaval T / Vives RR / Richard E / Henault J / Le Narvor C / Bonnaffe D / Priem B / Wild R / Lortat-Jacob H
History
DepositionMay 11, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17349.png

Downloads & links

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Map

FileDownload / File: emd_17349.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of human NDST1 homodimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 320 pix.
= 360. Å		1.13 Å/pix.
x 320 pix.
= 360. Å		1.13 Å/pix.
x 320 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.262
Minimum - Maximum-0.83742154 - 1.2649331
Average (Standard dev.)0.00012342552 (±0.028968407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17349_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from final non-uniform refinement

Fileemd_17349_half_map_1.map
AnnotationHalf map B from final non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from final non-uniform refinement

Fileemd_17349_half_map_2.map
AnnotationHalf map A from final non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NDST1 homodimer

EntireName: NDST1 homodimer
Components
  • Complex: NDST1 homodimer
    • Protein or peptide: N-deacetylase/N-sulfotransferase 1

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Supramolecule #1: NDST1 homodimer

SupramoleculeName: NDST1 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: N-deacetylase/N-sulfotransferase 1

MacromoleculeName: N-deacetylase/N-sulfotransferase 1 / type: protein_or_peptide / ID: 1
Details: Human NDST1 homodimer (residues 43-882), containing a linker and a 8-His tag at the C-terminus
Enantiomer: LEVO / EC number: [heparan sulfate]-glucosamine N-sulfotransferase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GASRGLEPSA DAPEPDCGDP PPVAPSRLLP LKPVQAATPS RTDPLVLVFV ESLYSQLGQE VVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY C VAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL ...String:
GASRGLEPSA DAPEPDCGDP PPVAPSRLLP LKPVQAATPS RTDPLVLVFV ESLYSQLGQE VVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY C VAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL YVTRPSEVEK GV LPGEDWT VFQSNHSTYE PVLLAKTRSS ESIPHLGADA GLHAALHATV VQDLGLHDGI QRV LFGNNL NFWLHKLVFV DAVAFLTGKR LSLPLDRYIL VDIDDIFVGK EGTRMKVEDV KALF DTQNE LRAHIPNFTF NLGYSGKFFH TGTNAEDAGD DLLLSYVKEF WWFPHMWSHM QPHLF HNQS VLAEQMALNK KFAVEHGIPT DMGYAVAPHH SGVYPVHVQL YEAWKQVWSI RVTSTE EYP HLKPARYRRG FIHNGIMVLP RQTCGLFTHT IFYNEYPGGS SELDKIINGG ELFLTVL LN PISIFMTHLS NYGNDRLGLY TFKHLVRFLH SWTNLRLQTL PPVQLAQKYF QIFSEEKD P LWQDPCEDKR HKDIWSKEKT CDRFPKLLII GPQKTGTTAL YLFLGMHPDL SSNYPSSET FEEIQFFNGH NYHKGIDWYM EFFPIPSNTT SDFYFEKSAN YFDSEVAPRR AAALLPKAKV LTILINPAD RAYSWYQHQR AHDDPVALKY TFHEVITAGS DASSKLRALQ NRCLVPGWYA T HIERWLSA YHANQILVLD GKLLRTEPAK VMDMVQKFLG VTNTIDYHKT LAFDPKKGFW CQ LLEGGKT KCLGKSKGRK YPEMDLDSRA FLKDYYRDHN IELSKLLYKM GQTLPTWLRE DLQ NTRNNN NNNGHHHHHH HH

UniProtKB: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1

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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

Concentration0.3 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
8.0 mMMES2-Morpholinoethanesulfonic acid
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: Current: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotted for 4 s with a blot force of 0.
DetailsProtein eluted as monodisperse peak from size exclusion chromatography column

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-44 / Number grids imaged: 1 / Number real images: 3038 / Average exposure time: 4.4 sec. / Average electron dose: 38.9 e/Å2
Details: Dataset was collected at a 30 degrees stage tilt angle
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3554427
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: non-uniform refinement / Number images used: 221316
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: ab initio
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: non-uniform refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1) / Software - details: ab initio reconstruction
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 65-882 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: Model of NDST1 homodimer was predicted using AlphaFold2
DetailsCCC 0.658
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient

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