+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43345 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human HGSNAT in inactive state | |||||||||
Map data | sharpened map | |||||||||
Sample |
| |||||||||
Keywords | Membrane 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 / 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 | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Li F | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome Authors: Li F | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_43345.map.gz | 307.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-43345-v30.xml emd-43345.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_43345.png | 96.7 KB | ||
Filedesc metadata | emd-43345.cif.gz | 5.9 KB | ||
Others | emd_43345_additional_1.map.gz emd_43345_half_map_1.map.gz emd_43345_half_map_2.map.gz | 161.3 MB 301.2 MB 301.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43345 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43345 | HTTPS FTP |
-Validation report
Summary document | emd_43345_validation.pdf.gz | 921.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_43345_full_validation.pdf.gz | 920.9 KB | Display | |
Data in XML | emd_43345_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_43345_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43345 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43345 | HTTPS FTP |
-Related structure data
Related structure data | 8vlvMC 8vkjC 8vlgC 8vliC 8vluC 8vlyC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_43345.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: unsharpened map used to build TM1 (residue 191-226)....
File | emd_43345_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpened map used to build TM1 (residue 191-226). All other area is built based on the sharpened map. The entire model, including TM1, is refined against the sharpened map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map
File | emd_43345_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map
File | emd_43345_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : purified human HGSNAT
Entire | Name: purified human HGSNAT |
---|---|
Components |
|
-Supramolecule #1: purified human HGSNAT
Supramolecule | Name: purified human HGSNAT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73 KDa |
-Macromolecule #1: Heparan-alpha-glucosaminide N-acetyltransferase
Macromolecule | Name: 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 weight | Theoretical: 73.365039 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 7 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.9 mg/mL |
---|---|
Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 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: 22.0 µm / Nominal defocus min: 10.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134353 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |