+Open data
-Basic information
Entry | Database: PDB / ID: 4ikm | |||||||||
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Title | X-ray structure of CARD8 CARD domain | |||||||||
Components | Maltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8 | |||||||||
Keywords | SIGNALING PROTEIN / Death fold superfamily / six-helix bundle / inflammasome / apoptosis / innate immune system / signal transduction | |||||||||
Function / homology | Function and homology information CARD8 inflammasome complex assembly / CARD8 inflammasome complex / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway ...CARD8 inflammasome complex assembly / CARD8 inflammasome complex / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis / Regulation of the apoptosome activity / Hydrolases; Acting on peptide bonds (peptidases) / regulation of canonical NF-kappaB signal transduction / negative regulation of interleukin-1 beta production / pattern recognition receptor activity / negative regulation of NF-kappaB transcription factor activity / detection of maltose stimulus / maltose transport complex / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate transport / cysteine-type endopeptidase activator activity involved in apoptotic process / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of tumor necrosis factor-mediated signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of canonical NF-kappaB signal transduction / antiviral innate immune response / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / peptidase activity / outer membrane-bounded periplasmic space / regulation of apoptotic process / defense response to virus / periplasmic space / DNA damage response / protein homodimerization activity / protein-containing complex / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4606 Å | |||||||||
Authors | Jin, T. / Huang, M. / Smith, P. / Jiang, J. / Xiao, T. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: The structure of the CARD8 caspase-recruitment domain suggests its association with the FIIND domain and procaspases through adjacent surfaces. Authors: Jin, T. / Huang, M. / 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 | 4ikm.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ikm.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ikm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/4ikm ftp://data.pdbj.org/pub/pdb/validation_reports/ik/4ikm | HTTPS FTP |
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-Related structure data
Related structure data | 3vd8S 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: 53368.055 Da / Num. of mol.: 1 / Fragment: MBP tagged human CARD8 CARD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Strain: K12 Gene: b4034, CARD8, TUCAN, CARDINAL, JW3994, malE, KIAA0955, NDPP1 Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: Q9Y2G2 | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 16% PEG8000, 0.1 M NaI, 0.1 M NaAc, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2012 |
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: 2.45→50 Å / Num. all: 21995 / Num. obs: 21951 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 3.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VD8 Resolution: 2.4606→47.438 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4606→47.438 Å
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Refine LS restraints |
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LS refinement shell |
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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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