+Open data
-Basic information
Entry | Database: PDB / ID: 4ifp | |||||||||
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Title | X-ray Crystal Structure of Human NLRP1 CARD Domain | |||||||||
Components | Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 1 | |||||||||
Keywords | IMMUNE SYSTEM / Death fold superfamily / inflammasome / signal transduction / innate immune system | |||||||||
Function / homology | Function and homology information NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B ...NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B / detection of maltose stimulus / maltose transport complex / pyroptotic inflammatory response / carbohydrate transport / cysteine-type endopeptidase activator activity involved in apoptotic process / response to muramyl dipeptide / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / signaling adaptor activity / antiviral innate immune response / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / double-stranded DNA binding / peptidase activity / outer membrane-bounded periplasmic space / neuron apoptotic process / regulation of apoptotic process / defense response to virus / periplasmic space / defense response to bacterium / protein domain specific binding / DNA damage response / nucleolus / apoptotic process / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9948 Å | |||||||||
Authors | Jin, T. / Curry, J. / Smith, P. / Jiang, J. / Xiao, T. | |||||||||
Citation | Journal: Proteins / Year: 2013 Title: Structure of the NLRP1 caspase recruitment domain suggests potential mechanisms for its association with procaspase-1. Authors: Jin, T. / Curry, J. / Smith, P. / Jiang, J. / Xiao, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ifp.cif.gz | 310.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ifp.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ifp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ifp_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4ifp_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4ifp_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 4ifp_validation.cif.gz | 96.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ifp ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ifp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 51696.559 Da / Num. of mol.: 3 / Fragment: NLRP1-CARD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Strain: K12 Gene: malE, b4034, JW3994, NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1 Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P0AEX9, UniProt: Q9C000 #2: Polysaccharide | #3: Chemical | #4: 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: 3.41 Å3/Da / Density % sol: 63.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.4 M Malonate, 100 mM HEPES 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97 Å |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9948→50 Å / Num. all: 140326 / Num. obs: 139624 / % possible obs: 99.5 % / Observed criterion σ(F): 1.65 / Observed criterion σ(I): 2.72 / Redundancy: 4.2 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9948→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.72 / Num. unique all: 6953 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VD8 and 3KAT Resolution: 1.9948→37.492 Å / SU ML: 0.19 / Cross valid method: Molprobity / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9948→37.492 Å
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Refine LS restraints |
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LS refinement shell |
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