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Yorodumi- EMDB-16223: Cryo-EM structure of the catalytic domain tetramer of N-terminall... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16223 | |||||||||
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Title | Cryo-EM structure of the catalytic domain tetramer of N-terminally truncated human tryptophan hydroxylase 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Serotonin biosynthesis / Tryptophan hydroxylase / aromatic amino acid hydroxylases / OXIDOREDUCTASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Zhang Z / Vedel IM / Skawinska NT / Harris P / Stark H / Peters GHJ | |||||||||
Funding support | Denmark, 1 items
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Citation | Journal: Structure / Year: 2023 Title: Structural characterization of human tryptophan hydroxylase 2 reveals that L-Phe is superior to L-Trp as the regulatory domain ligand. Authors: Ida M Vedel / Andreas Prestel / Zhenwei Zhang / Natalia T Skawinska / Holger Stark / Pernille Harris / Birthe B Kragelund / Günther H J Peters / Abstract: Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in serotonin biosynthesis in the brain. Consequently, regulation of TPH2 is relevant for serotonin-related diseases, yet the ...Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in serotonin biosynthesis in the brain. Consequently, regulation of TPH2 is relevant for serotonin-related diseases, yet the regulatory mechanism of TPH2 is poorly understood and structural and dynamical insights are missing. We use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared with the natural substrate, L-Trp. Using cryo-EM, we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM two-dimensional (2D) class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2's regulatory mechanism. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16223.map.gz | 139 MB | EMDB map data format | |
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Header (meta data) | emd-16223-v30.xml emd-16223.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_16223.png | 70.7 KB | ||
Others | emd_16223_half_map_1.map.gz emd_16223_half_map_2.map.gz | 139 MB 139 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16223 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16223 | HTTPS FTP |
-Validation report
Summary document | emd_16223_validation.pdf.gz | 593.5 KB | Display | EMDB validaton report |
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Full document | emd_16223_full_validation.pdf.gz | 593.1 KB | Display | |
Data in XML | emd_16223_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_16223_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16223 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16223 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16223.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16223_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16223_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 47 N-terminally truncated human tryptophan hydroxylase 2
Entire | Name: 47 N-terminally truncated human tryptophan hydroxylase 2 |
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Components |
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-Supramolecule #1: 47 N-terminally truncated human tryptophan hydroxylase 2
Supramolecule | Name: 47 N-terminally truncated human tryptophan hydroxylase 2 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 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: 4.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 197917 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |