+Open data
-Basic information
Entry | Database: PDB / ID: 5b5r | ||||||
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Title | Crystal structure of GSDMA3 | ||||||
Components | Gasdermin-A3 | ||||||
Keywords | TRANSPORT PROTEIN / pyroptosis excutioner | ||||||
Function / homology | Function and homology information sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / skin development / hair follicle morphogenesis ...sebaceous gland cell differentiation / avascular cornea development in camera-type eye / negative regulation of timing of anagen / hair cycle / wide pore channel activity / mammary gland development / positive regulation of extrinsic apoptotic signaling pathway / phosphatidylinositol-4-phosphate binding / skin development / hair follicle morphogenesis / phosphatidylserine binding / pyroptotic inflammatory response / somatic stem cell population maintenance / hair follicle development / extrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / mitochondrial membrane / negative regulation of canonical Wnt signaling pathway / defense response to bacterium / positive regulation of apoptotic process / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.902 Å | ||||||
Authors | Ding, J. / Shao, F. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Pore-forming activity and structural autoinhibition of the gasdermin family. Authors: Ding, J. / Wang, K. / Liu, W. / She, Y. / Sun, Q. / Shi, J. / Sun, H. / Wang, D.C. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5r.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5r.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 5b5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b5r_validation.pdf.gz | 282.7 KB | Display | wwPDB validaton report |
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Full document | 5b5r_full_validation.pdf.gz | 289 KB | Display | |
Data in XML | 5b5r_validation.xml.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5r ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52854.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdma3, Gsdm3 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5Y4Y6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-Tris (pH 6.5), 19% polyethylene glycol 3550, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 44110 / % possible obs: 97.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.902→37.914 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.31 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.902→37.914 Å
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Refine LS restraints |
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LS refinement shell |
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