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- PDB-8f0a: Client-bound structure of a DegP trimer within a 12mer cage -

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Basic information

Entry
Database: PDB / ID: 8f0a
TitleClient-bound structure of a DegP trimer within a 12mer cage
Components
  • (Periplasmic serine endoprotease DegP) x 2
  • Telomeric repeat-binding factor 1
KeywordsCHAPERONE / 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 / telomerase activity ...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 / telomerase activity / 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 / negative regulation of telomerase activity / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / programmed cell death / 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 Extension By Telomerase / telomere maintenance via 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 / telomere maintenance / serine-type peptidase activity / 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 / positive regulation of apoptotic process / cell division / serine-type endopeptidase activity / nucleolus / protein homodimerization activity / proteolysis / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Peptidase S1C, Do / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Peptidase S1C / Trypsin-like peptidase domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain ...Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Peptidase S1C, Do / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Peptidase S1C / Trypsin-like peptidase domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Homeobox-like domain superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsHarkness, R.W. / Ripstein, Z.A. / Di Trani, J.M. / Kay, L.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-503573 Canada
CitationJournal: 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
DepositionNov 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
a: Telomeric repeat-binding factor 1
b: Telomeric repeat-binding factor 1
c: Telomeric repeat-binding factor 1


Theoretical massNumber of molelcules
Total (without water)143,2919
Polymers143,2919
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Periplasmic serine endoprotease DegP / Heat shock protein DegP / Protease Do


Mass: 36376.176 Da / Num. of mol.: 3 / 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
#2: Protein Periplasmic serine endoprotease DegP / Heat shock protein DegP / Protease Do


Mass: 7970.229 Da / Num. of mol.: 3 / 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 Telomeric repeat-binding factor 1 / NIMA-interacting protein 2 / TTAGGG repeat-binding factor 1 / Telomeric protein Pin2/TRF1


Mass: 3417.168 Da / Num. of mol.: 3 / 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of a DegP trimer and the client protein hTRF1 from a 12mer cage structure
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 483190 / Symmetry type: POINT

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