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Open data
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Basic information
Entry | Database: PDB / ID: 8fy1 | |||||||||||||||||||||
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Title | E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2) | |||||||||||||||||||||
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![]() | TRANSCRIPTION / ternary complex / degrader | |||||||||||||||||||||
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 / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...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 / 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 / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cellular response to hypoxia / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / RHOBTB3 ATPase cycle / negative regulation of myeloid cell apoptotic process / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / transcription elongation factor activity / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / target-directed miRNA degradation / metanephros development / neuron maturation / elongin complex / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / VCB complex / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / response to iron ion / Replication of the SARS-CoV-1 genome / calcium ion transport into cytosol / channel activity / Cul5-RING ubiquitin ligase complex / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / organ growth / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / SUMOylation of ubiquitinylation proteins / B cell lineage commitment / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / negative regulation of transcription elongation by RNA polymerase II / T cell homeostasis / BH3 domain binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of calcium ion transport / B cell homeostasis / negative regulation of apoptotic signaling pathway / humoral immune response / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of anoikis / ubiquitin-like ligase-substrate adaptor activity / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Authors: Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Nayak, A. / Ruben, E.A. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.8 KB | Display | ![]() |
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PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 677.9 KB | Display | ![]() |
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Full document | ![]() | 684 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fy0C ![]() 8fy2C ![]() 6dc6S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20729.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13147.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 10843.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 23005.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Chemical | ChemComp-YF8 / Mass: 1640.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C82H104ClF3N11O11S4 / Feature type: SUBJECT OF INVESTIGATION |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 108 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→94.6 Å / Num. obs: 22772 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 55.35 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.56→2.68 Å / Num. unique obs: 2722 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DC6 Resolution: 2.56→80.5 Å / SU ML: 0.3737 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.2062 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→80.5 Å
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Refine LS restraints |
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LS refinement shell |
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