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Open data
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Basic information
Entry | Database: PDB / ID: 4m9z | ||||||
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Title | Crystal structure of CED-4 bound CED-3 fragment | ||||||
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![]() | APOPTOSIS / apoptosome | ||||||
Function / homology | ![]() BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / positive regulation of protein processing / caspase binding / embryonic morphogenesis / apoptotic process involved in development ...BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / positive regulation of protein processing / caspase binding / embryonic morphogenesis / apoptotic process involved in development / negative regulation of execution phase of apoptosis / actin filament depolymerization / activation of cysteine-type endopeptidase activity / embryo development ending in birth or egg hatching / regulation of cell size / muscle cell cellular homeostasis / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / endopeptidase activator activity / regulation of cell adhesion / regulation of protein stability / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / defense response to Gram-negative bacterium / positive regulation of apoptotic process / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, W.J. / Jinag, T.Y. / Choi, W.Y. / Wang, J.W. / Shi, Y.G. | ||||||
![]() | ![]() Title: Mechanistic insights into CED-4-mediated activation of CED-3. Authors: Huang, W. / Jiang, T. / Choi, W. / Qi, S. / Pang, Y. / Hu, Q. / Xu, Y. / Gong, X. / Jeffrey, P.D. / Wang, J. / Shi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426 KB | Display | ![]() |
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PDB format | ![]() | 349.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4m9rC ![]() 4m9sC ![]() 4m9xC ![]() 4m9yC ![]() 3lqqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 63797.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 975.024 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / Sequence details | SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM A OF UNIPROT P30429 (CED4_CAEEL, IDENTIFIER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.6-0.8M sodium acetate, 0.1M HEPES (pH 7.5), 0.1M sodium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97894 Å / Relative weight: 1 |
Reflection | Resolution: 3.405→50 Å / Num. obs: 48180 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.405→3.7 Å / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LQQ Resolution: 3.405→43.212 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 38.44 / 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: 3.405→43.212 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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