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Yorodumi- EMDB-16565: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16565 | |||||||||||||||||||||
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Title | Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (composite map and model) | |||||||||||||||||||||
Map data | Composite map after local refinements. Used for model building and refinement. | |||||||||||||||||||||
Sample |
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Keywords | Deacetylase / Sulfotransferase / Heparan Sulfate / Carbohydrate / Glycosaminoglycan / Nanobody | |||||||||||||||||||||
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 / trans-Golgi network membrane / forebrain development / cell population proliferation / positive regulation of MAPK cascade / inflammatory response / Golgi membrane / Golgi apparatus Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.42 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_16565.map.gz | 300 MB | EMDB map data format | |
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Header (meta data) | emd-16565-v30.xml emd-16565.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_16565.png | 62.3 KB | ||
Filedesc metadata | emd-16565.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16565 | HTTPS FTP |
-Validation report
Summary document | emd_16565_validation.pdf.gz | 639.1 KB | Display | EMDB validaton report |
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Full document | emd_16565_full_validation.pdf.gz | 638.7 KB | Display | |
Data in XML | emd_16565_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_16565_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16565 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16565 | HTTPS FTP |
-Related structure data
Related structure data | 8cd0MC 8ccyC 8chsC C: citing same article (ref.) M: atomic model generated by this map |
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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_16565.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map after local refinements. Used for model building and refinement. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Complex of heparan sulfate N-deacetylase-N-sulfotransferase 1 (wi...
Entire | Name: Complex of heparan sulfate N-deacetylase-N-sulfotransferase 1 (with ligands PAP and Mg2+) and nanobody nAb7 |
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Components |
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-Supramolecule #1: Complex of heparan sulfate N-deacetylase-N-sulfotransferase 1 (wi...
Supramolecule | Name: Complex of heparan sulfate N-deacetylase-N-sulfotransferase 1 (with ligands PAP and Mg2+) and nanobody nAb7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 100 KDa |
-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: 100.997617 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MPALACLRRL CRHVSPQAVL FLLFIFCLFS VFISAYYLYG WKRGLEPSAD APEPDCGDPP PVAPSRLLPL KPVQAATPSR TDPLVLVFV ESLYSQLGQE VVAILESSRF KYRTEIAPGK GDMPTLTDKG RGRFALIIYE NILKYVNLDA WNRELLDKYC V AYGVGIIG ...String: MPALACLRRL CRHVSPQAVL FLLFIFCLFS VFISAYYLYG WKRGLEPSAD APEPDCGDPP PVAPSRLLPL KPVQAATPSR TDPLVLVFV ESLYSQLGQE VVAILESSRF KYRTEIAPGK GDMPTLTDKG RGRFALIIYE NILKYVNLDA WNRELLDKYC V AYGVGIIG FFKANENSLL SAQLKGFPLF LHSNLGLKDC SINPKSPLLY VTRPSEVEKG VLPGEDWTVF QSNHSTYEPV LL AKTRSSE SIPHLGADAG LHAALHATVV QDLGLHDGIQ RVLFGNNLNF WLHKLVFVDA VAFLTGKRLS LPLDRYILVD IDD IFVGKE GTRMKVEDVK ALFDTQNELR AHIPNFTFNL GYSGKFFHTG TNAEDAGDDL LLSYVKEFWW FPHMWSHMQP HLFH NQSVL AEQMALNKKF AVEHGIPTDM GYAVAPHHSG VYPVHVQLYE AWKQVWSIRV TSTEEYPHLK PARYRRGFIH NGIMV LPRQ TCGLFTHTIF YNEYPGGSSE LDKIINGGEL FLTVLLNPIS IFMTHLSNYG NDRLGLYTFK HLVRFLHSWT NLRLQT LPP VQLAQKYFQI FSEEKDPLWQ DPCEDKRHKD IWSKEKTCDR FPKLLIIGPQ KTGTTALYLF LGMHPDLSSN YPSSETF EE IQFFNGHNYH KGIDWYMEFF PIPSNTTSDF YFEKSANYFD SEVAPRRAAA LLPKAKVLTI LINPADRAYS WYQHQRAH D DPVALKYTFH EVITAGSDAS SKLRALQNRC LVPGWYATHI ERWLSAYHAN QILVLDGKLL RTEPAKVMDM VQKFLGVTN TIDYHKTLAF DPKKGFWCQL LEGGKTKCLG KSKGRKYPEM DLDSRAFLKD YYRDHNIELS KLLYKMGQTL PTWLREDLQN TR UniProtKB: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 |
-Macromolecule #2: Nanobody nAb7
Macromolecule | Name: Nanobody nAb7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 17.656316 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG SVQAGGSLRL SCAASGFNVD DYAIGWFRQS PGKEREGVSC IGGDGTTYYE NSVKGRFTVS SDKRDNTVYL QMNNLRPED TAIYFCAADR SKYCVGKYFS TPSQYDFWGR GTHVTVSSEP KTPKPQPAAG PGGQHHHHHH GAEQKLISEE D LS |
-Macromolecule #3: ADENOSINE-3'-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-3'-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: A3P |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-A3P: |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 4 / 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
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 614944 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |