+Open data
-Basic information
Entry | Database: PDB / ID: 5agx | |||||||||
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Title | Bcl-2 alpha beta-1 LINEAR complex | |||||||||
Components |
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Keywords | APOPTOSIS / FOLDAMER / BIM | |||||||||
Function / homology | Function and homology information negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / regulation of glycoprotein biosynthetic process ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / RUNX3 regulates BCL2L11 (BIM) transcription / cochlear nucleus development / mesenchymal cell development / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / developmental pigmentation / positive regulation of neuron maturation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of osteoblast proliferation / positive regulation of fibroblast apoptotic process / gland morphogenesis / renal system process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / melanocyte differentiation / ear development / lymphoid progenitor cell differentiation / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / meiosis I / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / glomerulus development / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of T cell apoptotic process / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / oocyte development / negative regulation of execution phase of apoptosis / positive regulation of multicellular organism growth / tube formation / regulation of organ growth / neuron maturation / metanephros development / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / fertilization / negative regulation of B cell apoptotic process / negative regulation of ossification / response to UV-B / cellular response to glucocorticoid stimulus / response to iron ion / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / calcium ion transport into cytosol / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / channel activity / axon regeneration / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / organ growth / response to cycloheximide / digestive tract morphogenesis / : / branching involved in ureteric bud morphogenesis / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Smith, B.J. / F Lee, E. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Alpha Beta Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity on Living Cells Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / ...Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / Murphy, W.L. / Smith, B.J. / Gellman, S.H. / Fairlie, W.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5agx.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5agx.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 5agx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5agx ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5agx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19357.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-34,29-44,92-207 Source method: isolated from a genetically manipulated source Details: CONTAINS RESIDUES 1-34,92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817 | ||||
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#2: Protein | Mass: 19357.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-34,29-44,92-207 Source method: isolated from a genetically manipulated source Details: CONTAINS RESIDUES 1-34,92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817 | ||||
#3: Protein/peptide | Mass: 2711.190 Da / Num. of mol.: 2 / Fragment: BIM BH3, RESIDUES 146-166 / Source method: obtained synthetically Details: BIM BH3 WITH CYCLIC BETA AMINO ACIDS AT RESIDUES 2,6,16 AND PENTENY AMINO ACIDS AT RESIDUES 9,13 Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43521 #4: Water | ChemComp-HOH / | Sequence details | BCL-2 WITH THE UNSTRUCTUR | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE |
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Crystal grow | pH: 7 / Details: PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→40 Å / Num. obs: 20251 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 14 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.89 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED BCL-2 BECLIN BH3 COMPLEX Resolution: 2.24→40.009 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→40.009 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 96.644 Å / Origin y: 79.1155 Å / Origin z: 8.9341 Å
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Refinement TLS group | Selection details: ALL |