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Open data
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Basic information
Entry | Database: PDB / ID: 1pq1 | ||||||
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Title | Crystal structure of Bcl-xl/Bim | ||||||
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![]() | APOPTOSIS / Bcl-xl/Bim | ||||||
Function / homology | ![]() Activation of BIM and translocation to mitochondria / symbiont-mediated activation of host apoptosis => GO:0052151 / positive regulation of autophagy in response to ER overload / : / The NLRP1 inflammasome / leukocyte homeostasis / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / : ...Activation of BIM and translocation to mitochondria / symbiont-mediated activation of host apoptosis => GO:0052151 / positive regulation of autophagy in response to ER overload / : / The NLRP1 inflammasome / leukocyte homeostasis / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / : / lymphocyte homeostasis / BIM-BCL-xl complex / BIM-BCL-2 complex / NRAGE signals death through JNK / regulation of developmental pigmentation / positive regulation of synaptic vesicle clustering / RAS processing / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / BH domain binding / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / dendritic cell apoptotic process / ear development / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / meiosis I / mammary gland development / B cell apoptotic process / 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 / tube formation / regulation of organ growth / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / myeloid cell homeostasis / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / extrinsic component of membrane / dynein complex binding / positive regulation of ATP biosynthetic process / cellular response to alkaloid / hepatocyte apoptotic process / thymocyte apoptotic process / 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 / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / B cell homeostasis / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cell cycle / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / MDM2/MDM4 family protein binding / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / response to endoplasmic reticulum stress / mitochondrion organization / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / kidney development / cellular response to estradiol stimulus / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / response to virus / response to radiation / brain development / cellular response to gamma radiation / synaptic vesicle membrane / cellular response to amyloid-beta / 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 / presynapse Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W. | ||||||
![]() | ![]() Title: The structure of a Bcl-xl/Bim fragment complex: Implications for Bim function Authors: Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.5 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pq0SC 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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Components
#1: Protein | Mass: 22056.209 Da / Num. of mol.: 1 / Fragment: BIM Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4120.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: NH4H2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 18, 2002 |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 19877 / Num. obs: 19877 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1765 / % possible all: 90.9 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 90.9 % / Num. unique obs: 1765 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: mouse Bcl-xl, pdb entry 1PQ0 Resolution: 1.65→19.9 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.2048 Å2 / ksol: 0.393725 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.313 / Rfactor Rwork: 0.27 |