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Yorodumi- EMDB-23263: Cryo-EM map of pyridoxal 5'-phosphate synthase-like subunit PDX1.... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23263 | |||||||||
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Title | Cryo-EM map of pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis thaliana) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information pyridoxal phosphate biosynthetic process / protein heterodimerization activity / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Novikova IV / Evans JE | |||||||||
Funding support | United States, 2 items
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Citation | Journal: ACS Chem Biol / Year: 2021 Title: Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex. Authors: Irina V Novikova / Mowei Zhou / Chen Du / Marcelina Parra / Doo Nam Kim / Zachary L VanAernum / Jared B Shaw / Hanjo Hellmann / Vicki H Wysocki / James E Evans / Abstract: Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is ...Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23263.map.gz | 121.7 MB | EMDB map data format | |
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Header (meta data) | emd-23263-v30.xml emd-23263.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23263_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_23263.png | 56.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23263 | HTTPS FTP |
-Validation report
Summary document | emd_23263_validation.pdf.gz | 370.8 KB | Display | EMDB validaton report |
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Full document | emd_23263_full_validation.pdf.gz | 370.4 KB | Display | |
Data in XML | emd_23263_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_23263_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23263 | HTTPS FTP |
-Related structure data
Related structure data | 7lb5MC 7lb6C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23263.map.gz / Format: CCP4 / Size: 244.1 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: 0.759 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PDX1.2 dodecamer
Entire | Name: PDX1.2 dodecamer |
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Components |
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-Supramolecule #1: PDX1.2 dodecamer
Supramolecule | Name: PDX1.2 dodecamer / type: complex / ID: 1 / Parent: 0 Details: Native conditions. Buffer: 50 mM Tris, pH7.5, 150 mM NaCl, 4 mM DTT. |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Recombinant expression | Organism: Triticum aestivum (bread wheat) |
Molecular weight | Experimental: 449 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris, 150 mM NaCl, 4 mM DTT |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k 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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |