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Open data
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Basic information
Entry | Database: PDB / ID: 3io9 | ||||||
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Title | BimL12Y in complex with Mcl-1 | ||||||
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![]() | APOPTOSIS / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / Isopeptide bond / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation | ||||||
Function / homology | ![]() BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / BH domain binding / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / BH domain binding / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / channel activity / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / BH3 domain binding / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein transmembrane transporter activity / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / response to cytokine / kidney development / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / spermatogenesis / microtubule binding / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Czabotar, P.E. / Lee, E.F. / Yang, H. / Sleebs, B.E. / Lessene, G. / Colman, P.M. / Smith, B.J. / Fairlie, W.D. | ||||||
![]() | ![]() Title: Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind ligands. Authors: Lee, E.F. / Czabotar, P.E. / Yang, H. / Sleebs, B.E. / Lessene, G. / Colman, P.M. / Smith, B.J. / 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 | ![]() | 49.6 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3inqC ![]() 3io8C ![]() 2nl9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The asymmetric unit is the biological assembly |
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Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 1 Fragment: Fusion protein of mouse Mcl-1 residues 152-189 and human Mcl-1 residues 209-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MCL1, BCL2L3, Mcl1 / Plasmid details: GST-fusion / Plasmid: pGEX6P3 / Production host: ![]() ![]() | ||
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#2: Protein/peptide | Mass: 3324.707 Da / Num. of mol.: 1 / Fragment: BH3 peptide, residues 141-166 / Mutation: L152P / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) ![]() | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 0.15M zinc acetate, 0.15 M imidizole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2007 / Details: AXCO capillary optic |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 12417 / Num. obs: 11917 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 6 / Num. unique all: 1166 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2nl9 Resolution: 2.4→29.39 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.106 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.686 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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