[English] 日本語
Yorodumi
- EMDB-43348: Cryo-EM structure of human HGSNAT in transition state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43348
TitleCryo-EM structure of human HGSNAT in transition state
Map datasharpened map
Sample
  • Organelle or cellular component: purified human HGSNAT
    • Protein or peptide: Heparan-alpha-glucosaminide N-acetyltransferase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsMembrane protein / Lysosome / Transmembrane acetyltransferase / TRANSFERASE
Function / homology
Function and homology information


heparan-alpha-glucosaminide N-acetyltransferase / heparan-alpha-glucosaminide N-acetyltransferase activity / MPS IIIC - Sanfilippo syndrome C / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal transport / acyltransferase activity / protein complex oligomerization / tertiary granule membrane / specific granule membrane ...heparan-alpha-glucosaminide N-acetyltransferase / heparan-alpha-glucosaminide N-acetyltransferase activity / MPS IIIC - Sanfilippo syndrome C / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal transport / acyltransferase activity / protein complex oligomerization / tertiary granule membrane / specific granule membrane / lysosomal lumen / lysosomal membrane / Neutrophil degranulation / plasma membrane
Similarity search - Function
Heparan-alpha-glucosaminide N-acetyltransferase, catalytic domain / Heparan-alpha-glucosaminide N-acetyltransferase, catalytic
Similarity search - Domain/homology
Heparan-alpha-glucosaminide N-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsLi F / Zhao B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)K99MH119591 United States
Other private
CitationJournal: Nat Commun / Year: 2024
Title: Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome.
Authors: Boyang Zhao / Zhongzheng Cao / Yi Zheng / Phuong Nguyen / Alisa Bowen / Robert H Edwards / Robert M Stroud / Yi Zhou / Menno Van Lookeren Campagne / Fei Li /
Abstract: Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme ...Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Mutations of HGSNAT cause HS accumulation and consequently mucopolysaccharidosis IIIC, a devastating lysosomal storage disease characterized by progressive neurological deterioration and early death where no treatment is available. HGSNAT catalyzes a unique transmembrane acetylation reaction where the acetyl group of cytosolic acetyl-CoA is transported across the lysosomal membrane and attached to HS in one reaction. However, the reaction mechanism remains elusive. Here we report six cryo-EM structures of HGSNAT along the reaction pathway. These structures reveal a dimer arrangement and a unique structural fold, which enables the elucidation of the reaction mechanism. We find that a central pore within each monomer traverses the membrane and controls access of cytosolic acetyl-CoA to the active site at its luminal mouth where glucosamine binds. A histidine-aspartic acid catalytic dyad catalyzes the transfer reaction via a ternary complex mechanism. Furthermore, the structures allow the mapping of disease-causing variants and reveal their potential impact on the function, thus creating a framework to guide structure-based drug discovery efforts.
History
DepositionJan 12, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43348.png

Downloads & links

-
Map

FileDownload / File: emd_43348.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 366.96 Å		0.83 Å/pix.
x 440 pix.
= 366.96 Å		0.83 Å/pix.
x 440 pix.
= 366.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5915242 - 2.7976823
Average (Standard dev.)0.000771174 (±0.041738905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 366.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map

Fileemd_43348_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_43348_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : purified human HGSNAT

EntireName: purified human HGSNAT
Components
  • Organelle or cellular component: purified human HGSNAT
    • Protein or peptide: Heparan-alpha-glucosaminide N-acetyltransferase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: purified human HGSNAT

SupramoleculeName: purified human HGSNAT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73 KDa

-
Macromolecule #1: Heparan-alpha-glucosaminide N-acetyltransferase

MacromoleculeName: Heparan-alpha-glucosaminide N-acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: heparan-alpha-glucosaminide N-acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.365039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTGARASAAE QRRAGRSGQA RAAERAAGMS GAGRALAALL LAASVLSAAL LAPGGSSGRD AQAAPPRDLD KKRHAELKMD QALLLIHNE LLWTNLTVYW KSECCYHCLF QVLVNVPQSP KAGKPSAAAA SVSTQHGSIL QLNDTLEEKE VCRLEYRFGE F GNYSLLVK ...String:
MTGARASAAE QRRAGRSGQA RAAERAAGMS GAGRALAALL LAASVLSAAL LAPGGSSGRD AQAAPPRDLD KKRHAELKMD QALLLIHNE LLWTNLTVYW KSECCYHCLF QVLVNVPQSP KAGKPSAAAA SVSTQHGSIL QLNDTLEEKE VCRLEYRFGE F GNYSLLVK NIHNGVSEIA CDLAVNEDPV DSNLPVSIAF LIGLAVIIVI SFLRLLLSLD DFNNWISKAI SSRETDRLIN SE LGSPSRT DPLDGDVQPA TWRLSALPPR LRSVDTFRGI ALILMVFVNY GGGKYWYFKH ASWNGLTVAD LVFPWFVFIM GSS IFLSMT SILQRGCSKF RLLGKIAWRS FLLICIGIII VNPNYCLGPL SWDKVRIPGV LQRLGVTYFV VAVLELLFAK PVPE HCASE RSCLSLRDIT SSWPQWLLIL VLEGLWLGLT FLLPVPGCPT GYLGPGGIGD FGKYPNCTGG AAGYIDRLLL GDDHL YQHP SSAVLYHTEV AYDPEGILGT INSIVMAFLG VQAGKILLYY KARTKDILIR FTAWCCILGL ISVALTKVSE NEGFIP VNK NLWSLSYVTT LSSFAFFILL VLYPVVDVKG LWTGTPFFYP GMNSILVYVG HEVFENYFPF QWKLKDNQSH KEHLTQN IV ATALWVLIAY ILYRKKIFWK I

UniProtKB: Heparan-alpha-glucosaminide N-acetyltransferase

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.9 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 22.0 µm / Nominal defocus min: 10.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 226631
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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