[English] 日本語
Yorodumi
- EMDB-16661: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16661
TitleHuman heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb13 (original map)
Map dataNDST1-nAb13 complex. Original map before local refinements.
Sample
  • Complex: Human heparan sulfate N-deacetylase-N-sulfotransferase complex with nAb13
    • Complex: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
      • Protein or peptide: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
    • Complex: N-deacetylase-N-sulfotransferase 1
      • Protein or peptide: N-deacetylase-N-sulfotransferase 1
KeywordsDeacetylase / Sulfotransferase / Heparan Sulfate / Carbohydrate / Glycosaminoglycan / Nanobody
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 / cardiac septum development / glycosaminoglycan metabolic process ...[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 / cardiac septum development / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / deacetylase activity / 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) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsMycroft-West CJ / Wu L
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust218579/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V018523/1 United Kingdom
CitationJournal: 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
DepositionFeb 8, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16661.png

Downloads & links

-
Map

FileDownload / File: emd_16661.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNDST1-nAb13 complex. Original map before local refinements.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.47368726 - 0.73531723
Average (Standard dev.)0.00015924158 (±0.012296923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16661_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16661_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16661_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human heparan sulfate N-deacetylase-N-sulfotransferase complex wi...

EntireName: Human heparan sulfate N-deacetylase-N-sulfotransferase complex with nAb13
Components
  • Complex: Human heparan sulfate N-deacetylase-N-sulfotransferase complex with nAb13
    • Complex: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
      • Protein or peptide: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
    • Complex: N-deacetylase-N-sulfotransferase 1
      • Protein or peptide: N-deacetylase-N-sulfotransferase 1

-
Supramolecule #1: Human heparan sulfate N-deacetylase-N-sulfotransferase complex wi...

SupramoleculeName: Human heparan sulfate N-deacetylase-N-sulfotransferase complex with nAb13
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7

SupramoleculeName: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

-
Supramolecule #3: N-deacetylase-N-sulfotransferase 1

SupramoleculeName: N-deacetylase-N-sulfotransferase 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: N-deacetylase-N-sulfotransferase 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GSRTDPLVLV FVESLYSQLG QEVVAILES SRFKYRTEIA P GKGDMPTL TDKGRGRFAL II YENILKY VNLDAWNREL LDK YCVAYG VGIIGFFKAN ENSL LSAQL KGFPLFLHSN LGLKD CSIN PKSPLLYVTR PSEVEK GVL PGEDWTVFQS NHSTYEP VL ...String:
GSRTDPLVLV FVESLYSQLG QEVVAILES SRFKYRTEIA P GKGDMPTL TDKGRGRFAL II YENILKY VNLDAWNREL LDK YCVAYG VGIIGFFKAN ENSL LSAQL KGFPLFLHSN LGLKD CSIN PKSPLLYVTR PSEVEK GVL PGEDWTVFQS NHSTYEP VL LAKTRSSESI PHLGADAG L HAALHATVVQ DLGLHDGIQ RVLFGNNLNF WLHKLVFVDA VAFLTGKRL SLPLDRYILV D IDDIFVGK EGTRMKVEDV KA LFDTQNE LRAHIPNFTF NLG YSGKFF HTGTNAEDAG DDLL LSYVK EFWWFPHMWS HMQPH LFHN QSVLAEQMAL NKKFAV EHG IPTDMGYAVA PHHSGVY PV HVQLYEAWKQ VWSIRVTS T EEYPHLKPAR YRRGFIHNG IMVLPRQTCG LFTHTIFYNE YPGGSSELD KIINGGELFL T VLLNPISI FMTHLSNYGN DR LGLYTFK HLVRFLHSWT NLR LQTLPP VQLAQKYFQI FSEE KDPLW QDPCEDKRHK DIWSK EKTC DRFPKLLIIG PQKTGT TAL YLFLGMHPDL SSNYPSS ET FEEIQFFNGH NYHKGIDW Y MEFFPIPSNT TSDFYFEKS ANYFDSEVAP RRAAALLPKA KVLTILINP ADRAYSWYQH Q RAHDDPVA LKYTFHEVIT AG SDASSKL RALQNRCLVP GWY ATHIER WLSAYHANQI LVLD GKLLR TEPAKVMDMV QKFLG VTNT IDYHKTLAFD PKKGFW CQL LEGGKTKCLG KSKGRKY PE MDLDSRAFLK DYYRDHNI E LSKLLYKMGQ TLPTWLRED LQNTR(A3P)

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

-
Macromolecule #2: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7

MacromoleculeName: Nanobody nAb13 - all CA rigid fit model derived from nanobody nAb7
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG SVQAGGSLRL SCAASGFNVD DYAIGWFRQS PGKEREGVSC IGGDGTTYYE NSVKGRFTVS SDKRDNTVYL QMNNLRPEDT AIYFCAADRS KYCVGKYFST PSQYDFWGRG THVTVSSEPK TPKPQPAAGP GGQHHHHHHG AEQKLISEED LS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE
DetailsMonodisperse sample from size exclusion

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87798
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more