+Open data
-Basic information
Entry | Database: PDB / ID: 8f26 | ||||||
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Title | Structure of a 60mer DegP cage bound to the client protein hTRF1 | ||||||
Components |
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Keywords | CHAPERONE / HYDROLASE / Protease / cage / complex | ||||||
Function / homology | Function and homology information positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / peptidase Do / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / peptidase Do / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / chaperone-mediated protein folding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / serine-type peptidase activity / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / spindle / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / microtubule binding / response to oxidative stress / chromosome, telomeric region / periplasmic space / nuclear body / cell division / serine-type endopeptidase activity / nucleolus / protein homodimerization activity / proteolysis / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.7 Å | ||||||
Authors | Harkness, R.W. / Ripstein, Z.A. / Di Trani, J.M. / Kay, L.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J Am Chem Soc / Year: 2023 Title: Flexible Client-Dependent Cages in the Assembly Landscape of the Periplasmic Protease-Chaperone DegP. Authors: Robert W Harkness / Zev A Ripstein / Justin M Di Trani / Lewis E Kay / Abstract: The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram- ...The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram-negative bacteria and is essential to bacterial survival under stress conditions. To perform these functions, DegP captures clients inside cage-like structures, which we have recently shown to form through the reorganization of high-order preformed apo oligomers, consisting of trimeric building blocks, that are structurally distinct from client-bound cages. Our previous studies suggested that these apo oligomers may allow DegP to encapsulate clients of various sizes under protein folding stresses by forming ensembles that can include extremely large cage particles, but how this occurs remains an open question. To explore the relation between cage and substrate sizes, we engineered a series of DegP clients of increasing hydrodynamic radii and analyzed their influence on DegP cage formation. We used dynamic light scattering and cryogenic electron microscopy to characterize the hydrodynamic properties and structures of the DegP cages that are adopted in response to each client. We present a series of density maps and structural models that include those for novel particles of approximately 30 and 60 monomers. Key interactions between DegP trimers and the bound clients that stabilize the cage assemblies and prime the clients for catalysis are revealed. We also provide evidence that DegP can form cages which approach subcellular organelles in terms of size. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f26.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f26.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 8f26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f26_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8f26_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8f26_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 8f26_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f26 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f26 | HTTPS FTP |
-Related structure data
Related structure data | 28808MC 8f0aC 8f0uC 8f1tC 8f1uC 8f21C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 36376.176 Da / Num. of mol.: 1 / Fragment: protease and PDZ1 domains (UNP residues 38-385) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: degP, htrA, ptd, b0161, JW0157 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0V0, peptidase Do |
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#2: Protein | Mass: 7970.229 Da / Num. of mol.: 1 / Fragment: PDZ2 domain (UNP residues 400-474) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: degP, htrA, ptd, b0161, JW0157 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0V0, peptidase Do |
#3: Protein/peptide | Mass: 3417.168 Da / Num. of mol.: 1 / Fragment: UNP residues 404-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54274 |
-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: Structure of a 60mer DegP cage bound to the client protein hTRF1 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14443 / Symmetry type: POINT |