+Open data
-Basic information
Entry | Database: PDB / ID: 1cy5 | ||||||
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Title | CRYSTAL STRUCTURE OF THE APAF-1 CARD | ||||||
Components | PROTEIN (APOPTOTIC PROTEASE ACTIVATING FACTOR 1) | ||||||
Keywords | APOPTOSIS / CASPASE RECRUITMENT DOMAIN / DEATH FOLD / SIX ALPHA-HELIX BUNDLE / GREEK KEY TOPOLOGY | ||||||
Function / homology | Function and homology information response to G1 DNA damage checkpoint signaling / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases ...response to G1 DNA damage checkpoint signaling / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / 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 / 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 / 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 / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / neuron apoptotic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / positive regulation of apoptotic process / nucleotide binding / apoptotic process / Neutrophil degranulation / 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 / SYNCHROTRON / MAD PROGRAM PACKAGE USED (IF ANY) : SHARP STARTING MODEL FOR MOLECULAR REPLACEMENT: NONE / Resolution: 1.3 Å | ||||||
Authors | Vaughn, D.E. / Joshua-Tor, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of Apaf-1 caspase recruitment domain: an alpha-helical Greek key fold for apoptotic signaling. Authors: Vaughn, D.E. / Rodriguez, J. / Lazebnik, Y. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cy5.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cy5.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/1cy5 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/1cy5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11099.710 Da / Num. of mol.: 1 / Fragment: CASPASE RECRUITMENT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O14727 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BME / | #4: 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: 2.09 Å3/Da / Density % sol: 30 % Description: RESIDUES 93-97 ARE DISORDERED AND NOT MODELED. SEE JOURNAL REFERENCE FOR PHASING DETAILS |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0. ...Details: HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0.005 MOLAR 2-MERCAPTOETHANOL RESERVOIR SOLUTION: 8-20% (W/V) PEG 8000, 0.2 MOLAR TRIS (PH 7.5-8.0), 0.05-0.2 MOLAR ZINC ACETATE., VAPOR DIFFUSION, HANGING DROP, temperature 17K |
Crystal grow | *PLUS Method: vapor diffusion |
Components of the solutions | *PLUS Common name: zinc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 |
Detector | Type: ADSC / Detector: CCD / Date: Feb 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. obs: 24113 / % possible obs: 98 % / Observed criterion σ(I): -9 / Redundancy: 6 % / Rsym value: 0.026 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.3 / % possible all: 96 |
Reflection | *PLUS Num. measured all: 145226 / Rmerge(I) obs: 0.026 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD PROGRAM PACKAGE USED (IF ANY) : SHARP STARTING MODEL FOR MOLECULAR REPLACEMENT: NONE Resolution: 1.3→6 Å / Num. parameters: 7764 / Num. restraintsaints: 13719 / Cross valid method: FREE-R / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 741 / Occupancy sum non hydrogen: 853 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.169 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |