+Open data
-Basic information
Entry | Database: PDB / ID: 5ngi | ||||||
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Title | Structure of XcpQN012 | ||||||
Components | Type II secretion system protein D | ||||||
Keywords | TRANSPORT PROTEIN / Secretion system II / Pseudomonas aeruginosa / secretin N domain | ||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Cambillau, C. / Roussel, A. / Trinh, T.N. | ||||||
Funding support | France, 1items
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Citation | Journal: mBio / Year: 2017 Title: Unraveling the Self-Assembly of the XcpQ Secretin Periplasmic Domain Provides New Molecular Insights into Type II Secretion System Secreton Architecture and Dynamics. Authors: Badreddine Douzi / Nhung T T Trinh / Sandra Michel-Souzy / Aline Desmyter / Geneviève Ball / Pascale Barbier / Artemis Kosta / Eric Durand / Katrina T Forest / Christian Cambillau / Alain ...Authors: Badreddine Douzi / Nhung T T Trinh / Sandra Michel-Souzy / Aline Desmyter / Geneviève Ball / Pascale Barbier / Artemis Kosta / Eric Durand / Katrina T Forest / Christian Cambillau / Alain Roussel / Romé Voulhoux / Abstract: The type II secretion system (T2SS) releases large folded exoproteins across the envelope of many Gram-negative pathogens. This secretion process therefore requires specific gating, interacting, and ...The type II secretion system (T2SS) releases large folded exoproteins across the envelope of many Gram-negative pathogens. This secretion process therefore requires specific gating, interacting, and dynamics properties mainly operated by a bipartite outer membrane channel called secretin. We have a good understanding of the structure-function relationship of the pore-forming C-terminal domain of secretins. In contrast, the high flexibility of their periplasmic N-terminal domain has been an obstacle in obtaining the detailed structural information required to uncover its molecular function. In , the Xcp T2SS plays an important role in bacterial virulence by its capacity to deliver a large panel of toxins and degradative enzymes into the surrounding environment. Here, we revealed that the N-terminal domain of XcpQ secretin spontaneously self-assembled into a hexamer of dimers independently of its C-terminal domain. Furthermore, and by using multidisciplinary approaches, we elucidate the structural organization of the XcpQ N domain and demonstrate that secretin flexibility at interdimer interfaces is mandatory for its function. Bacterial secretins are large homooligomeric proteins constituting the outer membrane pore-forming element of several envelope-embedded nanomachines essential in bacterial survival and pathogenicity. They comprise a well-defined membrane-embedded C-terminal domain and a modular periplasmic N-terminal domain involved in substrate recruitment and connection with inner membrane components. We are studying the XcpQ secretin of the T2SS present in the pathogenic bacterium Our data highlight the ability of the XcpQ N-terminal domain to spontaneously oligomerize into a hexamer of dimers. Further experiments revealed that this domain adopts different conformations essential for the T2SS secretion process. These findings provide new insights into the functional understanding of bacterial T2SS secretins. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ngi.cif.gz | 169.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ngi.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 5ngi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ngi_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 5ngi_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 5ngi_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5ngi_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngi ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngi | HTTPS FTP |
-Related structure data
Related structure data | 3641C 3649C 5mp2C 4e9jS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25935.201 Da / Num. of mol.: 2 / Fragment: N domain, UNP residues 79-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: xcpQ1, PAMH19_1963 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8RG33, UniProt: P35818*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.8M lithium chloride, 0.1M Tris-HCl, pH 8.5, 0.1M sodium acetate, and 32% PEG 4000 (w/v). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→48.2 Å / Num. obs: 10400 / % possible obs: 99.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 124.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.98→3.16 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / Num. unique obs: 1659 / CC1/2: 0.982 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E9J Resolution: 2.98→48.16 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9497 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.351
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Displacement parameters | Biso mean: 137.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.993 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.98→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.98→3.33 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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