+Open data
-Basic information
Entry | Database: PDB / ID: 5vx2 | ||||||||||||
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Title | Mcl-1 in complex with Bim-h3Pc-RT | ||||||||||||
Components |
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Keywords | APOPTOSIS / Bcl-2 Family / Pro-surivial | ||||||||||||
Function / homology | Function and homology information 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 / cell fate determination / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / mitochondrial fusion / channel activity / 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 / BH3 domain binding / T cell homeostasis / 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 / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / kidney development / response to cytokine / positive regulation of protein-containing complex assembly / Signaling by ALK fusions and activated point mutants / 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 / microtubule binding / spermatogenesis / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | ||||||||||||
Authors | Cowan, A.D. / Brouwer, J.M. / Colman, P.M. / Czabotar, P.E. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Mol. Cell / Year: 2017 Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vx2.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vx2.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 5vx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/5vx2 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vx2 | HTTPS FTP |
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-Related structure data
Related structure data | 5vwvC 5vwwC 5vwxC 5vwyC 5vwzC 5vx0C 5vx1C 5vx3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 2 Fragment: UNP P97287 residues 152-189, UNP Q07820 residues 209-327 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: Mcl1, MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: P97287, UniProt: Q07820 #2: Protein/peptide | Mass: 3241.641 Da / Num. of mol.: 2 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion Details: 20 % PEG 3000, 100 mM trisodium citrate buffered with citric acid pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.851→32.25 Å / Num. obs: 34486 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 15.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.851→32.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.851→32.25 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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