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Yorodumi- PDB-4hnj: Crystallographic structure of BCL-xL domain-swapped dimer in comp... -
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-Basic information
Entry | Database: PDB / ID: 4hnj | ||||||
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Title | Crystallographic structure of BCL-xL domain-swapped dimer in complex with PUMA BH3 peptide at 2.9A resolution | ||||||
Components |
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Keywords | Apoptosis/PROTEIN BINDING / BCL2-family / domain-swapped dimer / apoptosis regulation / BCL-xL / PUMA / Apoptosis-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / T cell apoptotic process / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / T cell apoptotic process / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cysteine-type endopeptidase activity / fertilization / positive regulation of thymocyte apoptotic process / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / fibroblast apoptotic process / execution phase of apoptosis / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ectopic germ cell programmed cell death / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to hypoxia / spermatogenesis / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / defense response to virus / nuclear membrane / mitochondrial inner membrane / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / DNA damage response / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Fisher, J.C. / Yun, M.K. / White, S.W. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis. Authors: Follis, A.V. / Chipuk, J.E. / Fisher, J.C. / Yun, M.K. / Grace, C.R. / Nourse, A. / Baran, K. / Ou, L. / Min, L. / White, S.W. / Green, D.R. / Kriwacki, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hnj.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hnj.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 4hnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/4hnj ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hnj | HTTPS FTP |
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-Related structure data
Related structure data | 2m03C 2m04C 1r2dS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 23669.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817 #2: Protein/peptide | | Mass: 3053.326 Da / Num. of mol.: 1 / Fragment: BH3 domain peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1 #3: 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: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M CaCl2, 0.1 M NaOAc, 20% V/V isopropanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 21, 2006 | |||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. all: 11798 / Num. obs: 11326 / % possible obs: 96 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34 / Redundancy: 21.7 % / Rsym value: 0.094 / Net I/σ(I): 38.5 | |||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1R2D Resolution: 2.9→42.878 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7923 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 26.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.845 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 197.81 Å2 / Biso mean: 93.8646 Å2 / Biso min: 34.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→42.878 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: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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