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Open data
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Basic information
Entry | Database: PDB / ID: 6o0l | |||||||||
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Title | crystal structure of BCL-2 G101V mutation with venetoclax | |||||||||
![]() | Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2 | |||||||||
![]() | APOPTOSIS / BCL-2 / Venetoclax / complex / Protein-protein interface inhibitor / resistance mutation / FDA approved drug complex | |||||||||
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 / 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 / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / 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 / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism 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 / 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 / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic 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 / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / hepatocyte apoptotic process / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / regulation of calcium ion transport / B cell homeostasis / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of anoikis / 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 Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Birkinshaw, R.W. / Luo, C.S. / Colman, P.M. / Czabotar, P.E. | |||||||||
![]() | ![]() Title: Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations. Authors: Birkinshaw, R.W. / Gong, J.N. / Luo, C.S. / Lio, D. / White, C.A. / Anderson, M.A. / Blombery, P. / Lessene, G. / Majewski, I.J. / Thijssen, R. / Roberts, A.W. / Huang, D.C.S. / Colman, P.M. / Czabotar, P.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.9 KB | Display | ![]() |
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PDB format | ![]() | 107.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 999.4 KB | Display | ![]() |
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Full document | ![]() | 1002.8 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o0kC ![]() 6o0mC ![]() 6o0oC ![]() 6o0pC ![]() 6o0gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19399.637 Da / Num. of mol.: 2 / Mutation: G101V,G101V,G101V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 26.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 4% PEG4K, 35% PEG400, 0.08M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2018 |
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.51 Å / Num. obs: 12909 / % possible obs: 99.84 % / Redundancy: 3.8 % / CC1/2: 0.991 / Rrim(I) all: 0.1432 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1270 / CC1/2: 0.646 / % possible all: 99.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6O0G Resolution: 2.2→47.508 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.34 Details: Authors state that the data were processed and refined in spacegroup P21, despite being possible to merge and refine in orthorhombic spacegroup P212121. This was due to poorer refinement ...Details: Authors state that the data were processed and refined in spacegroup P21, despite being possible to merge and refine in orthorhombic spacegroup P212121. This was due to poorer refinement statistics in the orthorhombic spacegroup.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.508 Å
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Refine LS restraints |
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LS refinement shell |
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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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