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Yorodumi- PDB-7lb5: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lb5 | |||||||||
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Title | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis thaliana) | |||||||||
Components | Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 | |||||||||
Keywords | PLANT PROTEIN / pseudoenzyme / dodecamer / vitamin B6 | |||||||||
Function / homology | Function and homology information pyridoxal phosphate biosynthetic process / protein heterodimerization activity / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Novikova, I.V. / Evans, J.E. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lb5.cif.gz | 525.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lb5.ent.gz | 425.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lb5_validation.pdf.gz | 921.7 KB | Display | wwPDB validaton report |
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Full document | 7lb5_full_validation.pdf.gz | 945.1 KB | Display | |
Data in XML | 7lb5_validation.xml.gz | 84.5 KB | Display | |
Data in CIF | 7lb5_validation.cif.gz | 114.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/7lb5 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/7lb5 | HTTPS FTP |
-Related structure data
Related structure data | 23263MC 7lb6C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 37408.004 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX12, A37, PDX1L2, At3g16050, MSL1.3 / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q9ZNR6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PDX1.2 dodecamer / Type: COMPLEX Details: Native conditions. Buffer: 50 mM Tris, pH7.5, 150 mM NaCl, 4 mM DTT. Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.449 MDa / Experimental value: YES |
Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Triticum aestivum (bread wheat) |
Buffer solution | pH: 7.5 / Details: 50 mM Tris, 150 mM NaCl, 4 mM DTT |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: at 15 mA. / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 60 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 787982 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265224 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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