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Yorodumi- PDB-3d7v: Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d7v | ||||||
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Title | Crystal structure of Mcl-1 in complex with an Mcl-1 selective BH3 ligand | ||||||
Components |
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Keywords | APOPTOSIS / helical bundle / amphipathic helix / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / Membrane / Mitochondrion / Nucleus / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation | ||||||
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 / 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 ...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 / 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 / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cell fate determination / cellular homeostasis / 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 / BH domain binding / 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 / odontogenesis of dentin-containing tooth / BH3 domain binding / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / spermatogenesis / microtubule binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Lee, E.F. / Czabotar, P.E. / Colman, P.M. / Fairlie, W.D. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2008 Title: A novel BH3 ligand that selectively targets Mcl-1 reveals that apoptosis can proceed without Mcl-1 degradation. Authors: Lee, E.F. / Czabotar, P.E. / van Delft, M.F. / Michalak, E.M. / Boyle, M.J. / Willis, S.N. / Puthalakath, H. / Bouillet, P. / Colman, P.M. / Huang, D.C.S. / Fairlie, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d7v.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7v.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7v ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7v | HTTPS FTP |
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-Related structure data
Related structure data | 2nl9S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18227.592 Da / Num. of mol.: 1 / Fragment: Bcl-2 like domain, Myeloid Cell Leukemia 1 Source method: isolated from a genetically manipulated source Details: FUSION PROTEIN CONSISTS OF THE N-TERMINAL EXPRESSION TAGS (GPLGS), RESIDUES 171-208 (UNIPROT RESIDUES 152-189) FROM INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG (MOUSE) ...Details: FUSION PROTEIN CONSISTS OF THE N-TERMINAL EXPRESSION TAGS (GPLGS), RESIDUES 171-208 (UNIPROT RESIDUES 152-189) FROM INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG (MOUSE) AND RESIDUES 209-327 FROM INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 (HUMAN) Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Gene: MCL1 / Plasmid: pGEX6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P97287, UniProt: Q07820 | ||||
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#2: Protein/peptide | Mass: 3156.515 Da / Num. of mol.: 1 / Fragment: Bim BH3 / Mutation: L62A, F69A / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: O43521 | ||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | FUSION PROTEIN CONSISTS OF THE N-TERMINAL EXPRESSION TAGS (GPLGS), RESIDUES 171-208 (UNIPROT ...FUSION PROTEIN CONSISTS OF THE N-TERMINAL EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 0.2M Zinc Acetate, 0.2M Imidazole, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 24, 2006 / Details: Capillary optics (AXCO) |
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: 2.03→60.3 Å / Num. obs: 13365 / % possible obs: 98.71 % / Observed criterion σ(I): 5.6 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1357 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NL9 Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.474 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.178 / ESU R Free: 0.167 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.253 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.034→2.086 Å / Total num. of bins used: 20
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