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Yorodumi- PDB-5o2y: NMR structure of the calcium bound form of PulG, major pseudopili... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o2y | ||||||
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Title | NMR structure of the calcium bound form of PulG, major pseudopilin from Klebsiella oxytoca T2SS | ||||||
Components | General secretion pathway protein G | ||||||
Keywords | PROTEIN TRANSPORT / Klebsiella oxytoca T2SS / major pseudopilin / calcium | ||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Klebsiella oxytoca (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Lopez-Castilla, A. / Bardiaux, B. / Vitorge, B. / Thomassin, J.-L. / Zheng, W. / Yu, X. / Egelman, E.H. / Nilges, M. / Francetic, O. / Izadi-Pruneyre, N. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Microbiol / Year: 2017 Title: Structure of the calcium-dependent type 2 secretion pseudopilus. Authors: Aracelys López-Castilla / Jenny-Lee Thomassin / Benjamin Bardiaux / Weili Zheng / Mangayarkarasi Nivaskumar / Xiong Yu / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic / Abstract: Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of ...Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of inner membrane-anchored fibres called pseudopili. Although efficient pseudopilus assembly is essential for protein secretion, structure-based functional analyses are required to unravel the mechanistic link between these processes. Here, we report an atomic model for a T2SS pseudopilus from Klebsiella oxytoca, obtained by fitting the NMR structure of its calcium-bound subunit PulG into the ~5-Å-resolution cryo-electron microscopy reconstruction of assembled fibres. This structure reveals the comprehensive network of inter-subunit contacts and unexpected features, including a disordered central region of the PulG helical stem, and highly flexible C-terminal residues on the fibre surface. NMR, mutagenesis and functional analyses highlight the key role of calcium in PulG folding and stability. Fibre disassembly in the absence of calcium provides a basis for pseudopilus length control, essential for protein secretion, and supports the Archimedes screw model for the type 2 secretion mechanism. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o2y.cif.gz | 521.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o2y.ent.gz | 433 KB | Display | PDB format |
PDBx/mmJSON format | 5o2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o2y_validation.pdf.gz | 401.4 KB | Display | wwPDB validaton report |
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Full document | 5o2y_full_validation.pdf.gz | 497.5 KB | Display | |
Data in XML | 5o2y_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5o2y_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o2y ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o2y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12928.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: pulG, AB185_31145, SAMEA2273639_02747 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0G3SCW3 |
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#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.5 mM [U-99% 13C; U-99% 15N] PulG, 50 mM non-labeled HEPES, 50 mM non-labeled sodium chloride, 1 mM non-labeled CaCl2, 90% H2O/10% D2O Label: 15N_13C / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 7 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 15 |