+Open data
-Basic information
Entry | Database: PDB / ID: 4rhw | ||||||
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Title | Crystal structure of Apaf-1 CARD and caspase-9 CARD complex | ||||||
Components |
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Keywords | APOPTOSIS / death domain superfamily | ||||||
Function / homology | Function and homology information caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion ...caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / Constitutive Signaling by AKT1 E17K in Cancer / cysteine-type endopeptidase activator activity involved in apoptotic process / protein maturation / enzyme activator activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / signal transduction in response to DNA damage / forebrain development / positive regulation of apoptotic signaling pathway / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / response to ischemia / ADP binding / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / nervous system development / peptidase activity / neuron apoptotic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / response to lipopolysaccharide / cell differentiation / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / nucleotide binding / apoptotic process / DNA damage response / Neutrophil degranulation / protein kinase binding / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hu, Q. / Wu, D. / Yan, C. / Shi, Y. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014 Title: Molecular determinants of caspase-9 activation by the Apaf-1 apoptosome. Authors: Hu, Q. / Wu, D. / Chen, W. / Yan, Z. / Yan, C. / He, T. / Liang, Q. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rhw.cif.gz | 248.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rhw.ent.gz | 201.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhw ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhw | HTTPS FTP |
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-Related structure data
Related structure data | 3ygsS 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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Details | AUTHOR STATED THE BIOLOGICAL UNIT CONTAINS 7 APAF-1 CARDS AND 4 CASPASE-9 CARDS. BASED ON THEIR EXPERIMENTAL RESULTS, APAF-1 FORMS A HEPTAMER IN THE APOPTOSOME, AND IN THE HOLOENZYME FORMED BY THE APOPTOSOME AND CASPASE-9, THE MOLAR RATIO BETWEEN APAF-1 AND CASPASE-9 IS 7:4. HOWEVER, FURTHER VALIDATION IS REQUIRED. |
-Components
#1: Protein | Mass: 11099.710 Da / Num. of mol.: 4 / Fragment: card domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 / Production host: Escherichia coli (E. coli) / References: UniProt: O14727 #2: Protein | Mass: 12741.549 Da / Num. of mol.: 2 / Fragment: card domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP9, MCH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55211, caspase-9 #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 16, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 44040 / Num. obs: 43908 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3YGS Resolution: 2.1→23.774 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 29.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.32 Å2 / ksol: 0.408 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→23.774 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: 15
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Refinement TLS params. | Method: refined / Origin x: -16.1075 Å / Origin y: -22.2377 Å / Origin z: -0.0985 Å
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Refinement TLS group | Selection details: all |