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Yorodumi- PDB-3mqp: Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mqp | ||||||
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Title | Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide, Northeast Structural Genomics Consortium Target HR2930 | ||||||
Components |
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Keywords | APOPTOSIS / bcl-2 family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information : / : / response to dsRNA / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of glucose metabolic process / Activation of NOXA and translocation to mitochondria / regulation of mitochondrial membrane permeability ...: / : / response to dsRNA / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of glucose metabolic process / Activation of NOXA and translocation to mitochondria / regulation of mitochondrial membrane permeability / mitochondrial fusion / channel activity / T cell homeostasis / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway by p53 class mediator / Nuclear events stimulated by ALK signaling in cancer / cellular response to glucose starvation / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway / proteasomal protein catabolic process / release of cytochrome c from mitochondria / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to hypoxia / regulation of apoptotic process / defense response to virus / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Guan, R. / Xiao, R. / Zhao, L. / Acton, T.B. / Gelinas, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human BFL-1 in complex with NOXA BH3 peptide Authors: Guan, R. / Xiao, R. / Zhao, L. / Acton, T.B. / Gelinas, C. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mqp.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mqp.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 3mqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/3mqp ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mqp | HTTPS FTP |
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-Related structure data
Related structure data | 3i1hS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18628.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2A1, BCL2L5, BFL1, GRS, HBPA1 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q16548 |
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#2: Protein/peptide | Mass: 2983.468 Da / Num. of mol.: 1 / Fragment: NOXA BH3 peptide, residues 19-43 / Source method: obtained synthetically Details: This sequence occurs naturally in humans. Peptide was synthesized from a commercial peptide synthesis service. Source: (synth.) Homo sapiens (human) / References: UniProt: Q13794 |
#3: 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: 1.95 Å3/Da / Density % sol: 36.79 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 1.5 M Sodium Malonate, 0.1 M sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→30.3 Å / Num. all: 7559 / Num. obs: 7385 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 45.125 Å2 / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.06 / Num. unique all: 643 / % possible all: 84.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3I1H Resolution: 2.24→30.3 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.987 Å2 | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→30.3 Å
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