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Open data
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Basic information
Entry | Database: PDB / ID: 4m9s | ||||||
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Title | crystal structure of CED-4 bound CED-3 fragment | ||||||
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![]() | APOPTOSIS / apoptosome / CED-3 | ||||||
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 / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / defense response to Gram-negative bacterium / positive regulation of apoptotic process / apoptotic process / negative regulation of 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 | ![]() | 425.6 KB | Display | ![]() |
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PDB format | ![]() | 350.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 57.1 KB | Display | |
Data in CIF | ![]() | 82.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m9rC ![]() 4m9xC ![]() 4m9yC ![]() 4m9zC ![]() 3lqqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 1039.957 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: 3.1 Å3/Da / Density % sol: 60.32 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS and I_PLUS/MINUS COLUMNS |
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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: 3.2→50 Å / Num. obs: 56679 / % possible obs: 74.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 27.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LQQ Resolution: 3.207→40.849 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 38.79 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS and I_PLUS/MINUS COLUMNS
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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: 3.207→40.849 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: 20
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