+Open data
-Basic information
Entry | Database: PDB / ID: 2ygs | ||||||
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Title | CARD DOMAIN FROM APAF-1 | ||||||
Components | APOPTOTIC PROTEASE ACTIVATING FACTOR 1 | ||||||
Keywords | APOPTOSIS / CASPASE RECRUITMENT DOMAIN / APAF-1 / RECOGNITION | ||||||
Function / homology | Function and homology information response to G1 DNA damage checkpoint signaling / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TP53 Regulates Transcription of Caspase Activators and Caspases ...response to G1 DNA damage checkpoint signaling / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to nutrient / forebrain development / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / kidney development / neural tube closure / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / nervous system development / secretory granule lumen / neuron apoptotic process / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / positive regulation of apoptotic process / nucleotide binding / Neutrophil degranulation / apoptotic process / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.6 Å | ||||||
Authors | Shi, Y. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Authors: Qin, H. / Srinivasula, S.M. / Wu, G. / Fernandes-Alnemri, T. / Alnemri, E.S. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ygs.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ygs.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ygs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2ygs ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2ygs | HTTPS FTP |
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-Related 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: 10640.215 Da / Num. of mol.: 1 / Fragment: CASPASE RECRUITMENT DOMAIN (CARD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: APAF-1 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O14727 |
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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: 2.02 Å3/Da / Density % sol: 33 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 12452 / % possible obs: 98.6 % / Redundancy: 11 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.177 / % possible all: 93.2 |
Reflection | *PLUS Num. obs: 11042 / % possible obs: 96.8 % / Num. measured all: 92435 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 88.8 % / Rmerge(I) obs: 0.12 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Rfactor Rfree: 0.309 / % reflection Rfree: 5 % / Rfactor Rwork: 0.254 |