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Open data
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Basic information
Entry | Database: PDB / ID: 5agx | |||||||||
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Title | Bcl-2 alpha beta-1 LINEAR complex | |||||||||
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![]() | APOPTOSIS / FOLDAMER / BIM | |||||||||
Function / homology | ![]() 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 / RUNX3 regulates BCL2L11 (BIM) transcription / osteoblast proliferation / 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 / apoptotic process involved in embryonic digit morphogenesis / renal system process / 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 / melanocyte differentiation / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / 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 / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / glomerulus development / positive regulation of T cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / oocyte development / tube formation / positive regulation of multicellular organism growth / regulation of organ growth / metanephros development / neuron maturation / 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 ossification / negative regulation of B cell apoptotic process / response to UV-B / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / response to iron ion / negative regulation of protein localization to plasma membrane / regulation of growth / calcium ion transport into cytosol / channel activity / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / Bcl-2 family protein complex / axon regeneration / epithelial cell apoptotic process / myeloid cell homeostasis / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / FOXO-mediated transcription of cell death genes / organ growth / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NRAGE signals death through JNK / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Smith, B.J. / F Lee, E. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152 KB | Display | ![]() |
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PDB format | ![]() | 121.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 455.5 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() ![]() ![]() | ||||
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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.) ![]() ![]() ![]() | ||||
#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.) ![]() #4: Water | ChemComp-HOH / | Sequence details | BCL-2 WITH THE UNSTRUCTUR | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |