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- EMDB-36388: membrane proteins -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36388
Titlemembrane proteins
Map data
Sample
  • Complex: HGSNAT
    • Protein or peptide: x 1 types
  • Ligand: x 10 types
Keywordsenzyme / acetylation / MEMBRANE PROTEIN
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: 2.68 Å
AuthorsYu J / Ge JP / Xu RS
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: membrane proteins
Authors: Yu J / Ge JP / Xu RS
History
DepositionJun 2, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36388.png

Downloads & links

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Map

FileDownload / File: emd_36388.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.8066807 - 2.926582
Average (Standard dev.)0.00039637423 (±0.038986407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36388_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36388_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HGSNAT

EntireName: HGSNAT
Components
  • Complex: HGSNAT
    • Protein or peptide: Heparan-alpha-glucosaminide N-acetyltransferase
  • Ligand: ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-[[(2~{R},4~{R})-4-methyl-2-oxidanyl-3,4-dihydro-2~{H}-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
  • Ligand: COENZYME A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: TETRADECANE
  • Ligand: N-OCTANE
  • Ligand: CHOLESTEROL
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: HEPTANE
  • Ligand: HEXADECANE

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Supramolecule #1: HGSNAT

SupramoleculeName: HGSNAT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 77.183992 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 IGSGGGGSGG GGSGGGWSHP QFEKGGGSGG GSGGSAWSHP QFEK

UniProtKB: Heparan-alpha-glucosaminide N-acetyltransferase

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Macromolecule #3: ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-[[(2~{R...

MacromoleculeName: ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-[[(2~{R},4~{R})-4-methyl-2-oxidanyl-3,4-dihydro-2~{H}-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
type: ligand / ID: 3 / Number of copies: 2 / Formula: UV6
Molecular weightTheoretical: 383.393 Da

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Macromolecule #4: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 4 / Number of copies: 2 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

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Macromolecule #6: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 6 / Number of copies: 24 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #7: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 7 / Number of copies: 32 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #8: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #9: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 9 / Number of copies: 2 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #10: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 10 / Number of copies: 6 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #11: HEPTANE

MacromoleculeName: HEPTANE / type: ligand / ID: 11 / Number of copies: 2 / Formula: HP6
Molecular weightTheoretical: 100.202 Da
Chemical component information

ChemComp-HP6:
HEPTANE

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Macromolecule #12: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 12 / Number of copies: 2 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 676337
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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