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Yorodumi- EMDB-27288: Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27288 | |||||||||
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Title | Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved catalytic loops | |||||||||
Map data | Human PRPS1 with Phosphate, ATP, and R5P; Hexamer Centered with resolved catalytic loops | |||||||||
Sample |
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Keywords | phosphoribosyl pyrophosphate synthetase / ATP and R5P substrates / catalytic loop / TRANSFERASE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Hvorecny KL / Kollman JM | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Human PRPS1 filaments stabilize allosteric sites to regulate activity. Authors: Kelli L Hvorecny / Kenzee Hargett / Joel D Quispe / Justin M Kollman / Abstract: The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and ...The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and mutations in the human enzyme PRPS1 lead to a spectrum of diseases. Here we determine structures of human PRPS1 filaments in active and inhibited states, with fixed assembly contacts accommodating both conformations. The conserved assembly interface stabilizes the binding site for the essential activator phosphate, increasing activity in the filament. Some disease mutations alter assembly, supporting the link between filament stability and activity. Structures of active PRPS1 filaments turning over substrate also reveal coupling of catalysis in one active site with product release in an adjacent site. PRPS1 filaments therefore provide an additional layer of allosteric control, conserved throughout evolution, with likely impact on metabolic homeostasis. Stabilization of allosteric binding sites by polymerization adds to the growing diversity of assembly-based enzyme regulatory mechanisms. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27288.map.gz | 13.3 MB | EMDB map data format | |
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Header (meta data) | emd-27288-v30.xml emd-27288.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_27288.png | 118.5 KB | ||
Filedesc metadata | emd-27288.cif.gz | 5 KB | ||
Others | emd_27288_half_map_1.map.gz emd_27288_half_map_2.map.gz | 97.8 MB 97.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27288 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27288 | HTTPS FTP |
-Validation report
Summary document | emd_27288_validation.pdf.gz | 802.7 KB | Display | EMDB validaton report |
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Full document | emd_27288_full_validation.pdf.gz | 802.2 KB | Display | |
Data in XML | emd_27288_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_27288_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27288 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27288 | HTTPS FTP |
-Related structure data
Related structure data | 8dbcC 8dbdC 8dbeC 8dbfC 8dbgC 8dbhC 8dbiC 8dbjC 8dbkC 8dblC 8dbmC 8dbnC 8dboC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27288.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Human PRPS1 with Phosphate, ATP, and R5P; Hexamer Centered with resolved catalytic loops | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Human PRPS1 with Phosphate, ATP, and R5P; Hexamer...
File | emd_27288_half_map_1.map | ||||||||||||
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Annotation | Human PRPS1 with Phosphate, ATP, and R5P; Hexamer Centered with resolved catalytic loops half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Human PRPS1 with Phosphate, ATP, and R5P; Hexamer...
File | emd_27288_half_map_2.map | ||||||||||||
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Annotation | Human PRPS1 with Phosphate, ATP, and R5P; Hexamer Centered with resolved catalytic loops half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hexamer of phosphoribosyl pyrophosphate synthetase 1 with phospha...
Entire | Name: Hexamer of phosphoribosyl pyrophosphate synthetase 1 with phosphate, ATP, and R5P; resolved catalytic loops |
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Components |
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-Supramolecule #1: Hexamer of phosphoribosyl pyrophosphate synthetase 1 with phospha...
Supramolecule | Name: Hexamer of phosphoribosyl pyrophosphate synthetase 1 with phosphate, ATP, and R5P; resolved catalytic loops type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Six copies of PRPS1 assemble to form a hexamer; hexamers assembly linearly to form filaments. Here, two of the catalytic loops are well resolved. |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Human Phosphoribosyl Pyrophosphate Synthetase 1
Macromolecule | Name: Human Phosphoribosyl Pyrophosphate Synthetase 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLME LLIMINACKI ASASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA G ADHIITMD LHASQIQGFF DIPVDNLYAE PAVLKWIREN ISEWRNCTIV ...String: MPNIKIFSGS SHQDLSQKIA DRLGLELGKV VTKKFSNQET CVEIGESVRG EDVYIVQSGC GEINDNLME LLIMINACKI ASASRVTAVI PCFPYARQDK KDKSRAPISA KLVANMLSVA G ADHIITMD LHASQIQGFF DIPVDNLYAE PAVLKWIREN ISEWRNCTIV SPDAGGAKRV TS IADRLNV DFALIHKERK KANEVDRMVL VGDVKDRVAI LVDDMADTCG TICHAADKLL SAG ATRVYA ILTHGIFSGP AISRINNACF EAVVVTNTIP QEDKMKHCSK IQVIDISMIL AEAI RRTHN GESVSYLFSH VPL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 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: 1.6 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PHENIX (ver. 1.18) / Number images used: 912162 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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