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Yorodumi- EMDB-15853: Tetrameric structure of 47 N-terminally truncated human tryptopha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15853 | |||||||||
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Title | Tetrameric structure of 47 N-terminally truncated human tryptophan hydroxylase 2 with dimerized regulatory domains | |||||||||
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Sample |
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Keywords | Tryptophan hydroxylase 2 / serotonin biosynthesis / OXIDOREDUCTASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 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_15853.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-15853-v30.xml emd-15853.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_15853.png | 45.8 KB | ||
Others | emd_15853_half_map_1.map.gz emd_15853_half_map_2.map.gz | 1.4 MB 1.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15853 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15853 | HTTPS FTP |
-Validation report
Summary document | emd_15853_validation.pdf.gz | 614.9 KB | Display | EMDB validaton report |
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Full document | emd_15853_full_validation.pdf.gz | 614.4 KB | Display | |
Data in XML | emd_15853_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_15853_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15853 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15853 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15853.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15853_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15853_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tryptophan 5-hydroxylase 2
Entire | Name: Tryptophan 5-hydroxylase 2 |
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Components |
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-Supramolecule #1: Tryptophan 5-hydroxylase 2
Supramolecule | Name: Tryptophan 5-hydroxylase 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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: 78.0 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 / Details: ab initio 3D |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58616 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |