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Yorodumi- EMDB-16564: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16564 | |||||||||||||||||||||
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Title | Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium and 3'-phosphoadenosine-5'-phosphosulfate | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | Deacetylase / Sulfotransferase / Heparan Sulfate / Carbohydrate / Glycosaminoglycan | |||||||||||||||||||||
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 neurocranium morphogenesis / embryonic viscerocranium 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 neurocranium morphogenesis / embryonic viscerocranium 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 | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||||||||
Authors | Mycroft-West CJ / Wu L | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1. Authors: Courtney J Mycroft-West / Sahar Abdelkarim / Helen M E Duyvesteyn / Neha S Gandhi / Mark A Skidmore / Raymond J Owens / Liang Wu / Abstract: Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, ...Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16564.map.gz | 301.7 MB | EMDB map data format | |
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Header (meta data) | emd-16564-v30.xml emd-16564.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16564_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_16564.png | 61.8 KB | ||
Masks | emd_16564_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-16564.cif.gz | 6.3 KB | ||
Others | emd_16564_half_map_1.map.gz emd_16564_half_map_2.map.gz | 301.4 MB 301.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16564 | HTTPS FTP |
-Validation report
Summary document | emd_16564_validation.pdf.gz | 901.6 KB | Display | EMDB validaton report |
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Full document | emd_16564_full_validation.pdf.gz | 901.2 KB | Display | |
Data in XML | emd_16564_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | emd_16564_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16564 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16564 | HTTPS FTP |
-Related structure data
Related structure data | 8ccyMC 8cd0C 8chsC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16564.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16564_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16564_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16564_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human heparan sulfate N-deacetylase-N-sulfotransferase 1
Entire | Name: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 |
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Components |
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-Supramolecule #1: Human heparan sulfate N-deacetylase-N-sulfotransferase 1
Supramolecule | Name: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
Macromolecule | Name: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 92.407461 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: SRTDPLVLVF VESLYSQLGQ EVVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY CVAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL YVTRPSEVEK GVLPGEDWTV FQSNHSTYEP V LLAKTRSS ...String: SRTDPLVLVF VESLYSQLGQ EVVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY CVAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL YVTRPSEVEK GVLPGEDWTV FQSNHSTYEP V LLAKTRSS ESIPHLGADA GLHAALHATV VQDLGLHDGI QRVLFGNNLN FWLHKLVFVD AVAFLTGKRL SLPLDRYILV DI DDIFVGK EGTRMKVEDV KALFDTQNEL RAHIPNFTFN LGYSGKFFHT GTNAEDAGDD LLLSYVKEFW WFPHMWSHMQ PHL FHNQSV LAEQMALNKK FAVEHGIPTD MGYAVAPHHS GVYPVHVQLY EAWKQVWSIR VTSTEEYPHL KPARYRRGFI HNGI MVLPR QTCGLFTHTI FYNEYPGGSS ELDKIINGGE LFLTVLLNPI SIFMTHLSNY GNDRLGLYTF KHLVRFLHSW TNLRL QTLP PVQLAQKYFQ IFSEEKDPLW QDPCEDKRHK DIWSKEKTCD RFPKLLIIGP QKTGTTALYL FLGMHPDLSS NYPSSE TFE EIQFFNGHNY HKGIDWYMEF FPIPSNTTSD FYFEKSANYF DSEVAPRRAA ALLPKAKVLT ILINPADRAY SWYQHQR AH DDPVALKYTF HEVITAGSDA SSKLRALQNR CLVPGWYATH IERWLSAYHA NQILVLDGKL LRTEPAKVMD MVQKFLGV T NTIDYHKTLA FDPKKGFWCQ LLEGGKTKCL GKSKGRKYPE MDLDSRAFLK DYYRDHNIEL SKLLYKMGQT LPTWLREDL QNTR UniProtKB: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 |
-Macromolecule #2: ADENOSINE-3'-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-3'-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: A3P |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-A3P: |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 23 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 6.5 |
Vitrification | Cryogen name: ETHANE |
Details | Monodisperse sample from size exclusion |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |