+Open data
-Basic information
Entry | Database: PDB / ID: 8vlv | |||||||||
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Title | Cryo-EM structure of human HGSNAT in inactive state | |||||||||
Components | Heparan-alpha-glucosaminide N-acetyltransferase | |||||||||
Keywords | MEMBRANE PROTEIN / TRANSFERASE / Lysosome / Transmembrane acetyltransferase | |||||||||
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 / tertiary granule membrane / specific granule membrane / lysosomal lumen ...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 / tertiary granule membrane / specific granule membrane / lysosomal lumen / protein complex oligomerization / lysosomal membrane / Neutrophil degranulation / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Li, F. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome Authors: Li, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vlv.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vlv.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vlv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8vlv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8vlv_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 8vlv_validation.cif.gz | 64.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/8vlv ftp://data.pdbj.org/pub/pdb/validation_reports/vl/8vlv | HTTPS FTP |
-Related structure data
Related structure data | 43345MC 8vkjC 8vlgC 8vliC 8vluC 8vlyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 73365.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGSNAT, TMEM76 / Production host: Homo sapiens (human) References: UniProt: Q68CP4, heparan-alpha-glucosaminide N-acetyltransferase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: purified human HGSNAT / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.073 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 22000 nm / Nominal defocus min: 10000 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134353 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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