+Open data
-Basic information
Entry | Database: PDB / ID: 3inq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of BCL-XL in complex with W1191542 | ||||||
Components | Bcl-2-like protein 1 | ||||||
Keywords | APOPTOSIS / Alternative splicing / Membrane / Mitochondrion / Nucleus / Transmembrane | ||||||
Function / homology | Function and homology information apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / epithelial cell proliferation / negative regulation of autophagy / cellular response to amino acid stimulus / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / response to cytokine / cellular response to gamma radiation / synaptic vesicle membrane / RAS processing / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear membrane / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fairlie, W.D. / Smith, B.J. / Colman, P.M. / Czabotar, P.E. / Lee, E.F. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3inq.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3inq.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 3inq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3inq_validation.pdf.gz | 975.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3inq_full_validation.pdf.gz | 982.9 KB | Display | |
Data in XML | 3inq_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3inq_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3inq ftp://data.pdbj.org/pub/pdb/validation_reports/in/3inq | HTTPS FTP |
-Related structure data
Related structure data | 3io8C 3io9C 3fdlS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17917.959 Da / Num. of mol.: 2 / Fragment: residues 1-209 / Mutation: DELETION OF AMINO ACIDS 27 TO 82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL-X / Plasmid: PGEX-6P3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07817 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Sequence details | BCL-XL WITH AMINO ACIDS 27 TO 82 DELETED AND A C-TERMINAL TRUNCATION OF THE LAST 24 RESIDUES THE ...BCL-XL WITH AMINO ACIDS 27 TO 82 DELETED AND A C-TERMINAL TRUNCATION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M Calcium Acetate, 10%(w/v) PEG8000, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 27, 2008 / 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→50 Å / Num. all: 39811 / Num. obs: 21237 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FDL Resolution: 2→31.63 Å / SU ML: 0.58 / σ(F): 1.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.081 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|