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Yorodumi- PDB-7acv: SLPL/HID (LMW SLP complex with HMW SLP interacting domain - HID) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7acv | ||||||
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Title | SLPL/HID (LMW SLP complex with HMW SLP interacting domain - HID) from C. difficile (R7404 strain) | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / bacterial surface layer protein / SLP LMW / SLP HMW interacting domain (HID) | ||||||
Function / homology | : / Low molecular weight S layer protein, N-terminal / Low molecular weight S layer protein, N-terminal, subdomain / Low molecular weight S layer protein N terminal / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / outer membrane-bounded periplasmic space / S-layer protein Function and homology information | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Barwinska-Sendra, A. / Lanzoni-Mangutchi, P. / Salgado, P.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure and assembly of the S-layer in C. difficile. Authors: Paola Lanzoni-Mangutchi / Oishik Banerji / Jason Wilson / Anna Barwinska-Sendra / Joseph A Kirk / Filipa Vaz / Shauna O'Beirne / Arnaud Baslé / Kamel El Omari / Armin Wagner / Neil F ...Authors: Paola Lanzoni-Mangutchi / Oishik Banerji / Jason Wilson / Anna Barwinska-Sendra / Joseph A Kirk / Filipa Vaz / Shauna O'Beirne / Arnaud Baslé / Kamel El Omari / Armin Wagner / Neil F Fairweather / Gillian R Douce / Per A Bullough / Robert P Fagan / Paula S Salgado / Abstract: Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, ...Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, the main S-layer protein of the bacterial pathogen Clostridioides difficile, and use electron microscopy to study S-layer organisation and assembly. The SlpA crystal lattice mimics S-layer assembly in the cell, through tiling of triangular prisms above the cell wall, interlocked by distinct ridges facing the environment. Strikingly, the array is very compact, with pores of only ~10 Å in diameter, compared to other S-layers (30-100 Å). The surface-exposed flexible ridges are partially dispensable for overall structure and assembly, although a mutant lacking this region becomes susceptible to lysozyme, an important molecule in host defence. Thus, our work gives insights into S-layer organisation and provides a basis for development of C. difficile-specific therapeutics. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7acv.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7acv.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 7acv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7acv_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 7acv_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 7acv_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 7acv_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/7acv ftp://data.pdbj.org/pub/pdb/validation_reports/ac/7acv | HTTPS FTP |
-Related structure data
Related structure data | 7acwC 7acxC 7acyC 7aczC 7qgqC 3cvzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34021.891 Da / Num. of mol.: 2 / Fragment: LMW SLP from C. difficile S-layer Source method: isolated from a genetically manipulated source Details: RT017, SLCT7b / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Variant: R7404 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase #2: Protein/peptide | | Mass: 5766.458 Da / Num. of mol.: 1 Fragment: HID - Interacting domain of HMW SLP (SLPH) from C. difficile S-layer Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: slpA, SAMEA708418_00075 / Variant: R7404 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9AEM2, N-acetylmuramoyl-L-alanine amidase #3: Water | ChemComp-HOH / | Compound details | Chain B could not be fully traced in the electron density maps, with considerable regions beyond ...Chain B could not be fully traced in the electron density maps, with considerable regions beyond residue 110 not modelled. | |
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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: 2.48 Å3/Da / Density % sol: 50.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, 0.1 M MES pH6.5, 35 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→86.35 Å / Num. obs: 29460 / % possible obs: 99.54 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.979 / Net I/σ(I): 5.48 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2924 / CC1/2: 0.713 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CVZ, D_1292110990 Resolution: 2.4→86.2 Å / SU ML: 0.4131 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.9679 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→86.2 Å
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Refine LS restraints |
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LS refinement shell |
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