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Yorodumi- PDB-8hla: Heteromeric ring comprised of peroxiredoxin from Thermococcus kod... -
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-Basic information
Entry | Database: PDB / ID: 8hla | ||||||
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Title | Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F76C) (Naph@(MIX|3:3)) | ||||||
Components | (Peroxiredoxin) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Peroxiredoxin / Complex / Protein protein interactions | ||||||
Function / homology | Function and homology information cellular response to stress / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis KOD1 (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å | ||||||
Authors | Himiyama, T. / Hamaguchi, T. / Yonekura, K. / Nakamura, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Bioconjug Chem / Year: 2023 Title: Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins. Authors: Tomoki Himiyama / Tasuku Hamaguchi / Koji Yonekura / Tsutomu Nakamura / Abstract: In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein ...In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from , which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hla.cif.gz | 446.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hla.ent.gz | 374.2 KB | Display | PDB format |
PDBx/mmJSON format | 8hla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hla_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8hla_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8hla_validation.xml.gz | 92.3 KB | Display | |
Data in CIF | 8hla_validation.cif.gz | 136.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/8hla ftp://data.pdbj.org/pub/pdb/validation_reports/hl/8hla | HTTPS FTP |
-Related structure data
Related structure data | 34859MC 8hh0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 24585.141 Da / Num. of mol.: 6 / Mutation: C46S,F76C,C205S,C211S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Gene: TK0537 / Production host: Escherichia coli (E. coli) References: UniProt: Q5JF30, thioredoxin-dependent peroxiredoxin #2: Protein | Mass: 24585.143 Da / Num. of mol.: 6 / Mutation: F42C,C46S,C205S,C211S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Gene: TK0537 / Production host: Escherichia coli (E. coli) References: UniProt: Q5JF30, thioredoxin-dependent peroxiredoxin #3: Chemical | ChemComp-FL3 / Has ligand of interest | Y | |
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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: Naph@MIX / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermococcus kodakarensis KOD1 (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (min): 89 K |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: In-column Omega Filter |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 599283 / Symmetry type: POINT | ||||||||||||||||||||||||
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