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Open data
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Basic information
Entry | Database: PDB / ID: 5c3g | ||||||
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Title | Crystal structure of Bcl-xl bound to BIM-MM | ||||||
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![]() | APOPTOSIS / Complex / Bcl-2 Family / BH3 / Stapled Peptide | ||||||
Function / homology | ![]() The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / positive regulation of synaptic vesicle clustering / RAS processing / RUNX3 regulates BCL2L11 (BIM) transcription ...The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / positive regulation of synaptic vesicle clustering / RAS processing / 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 / apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / 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 / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of T cell apoptotic process / 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 / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / FOXO-mediated transcription of cell death genes / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of ATP biosynthetic process / NRAGE signals death through JNK / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / 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 / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / endomembrane system / 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 / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / 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 / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / response to virus / response to radiation / cellular response to gamma radiation / synaptic vesicle membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miles, J.A. / Yeo, D.J. / Rowell, P. / Rodriguez-Marin, S. / Pask, C.M. / Warriner, S.L. / Edwards, T.A. / Wilson, A.J. | ||||||
![]() | ![]() Title: Hydrocarbon constrained peptides - understanding preorganisation and binding affinity. Authors: Miles, J.A. / Yeo, D.J. / Rowell, P. / Rodriguez-Marin, S. / Pask, C.M. / Warriner, S.L. / Edwards, T.A. / Wilson, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
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Full document | ![]() | 423.6 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c3fC ![]() 3fdlS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17506.504 Da / Num. of mol.: 1 / Fragment: UNP residues 1-26,UNP residues 83-209 Source method: isolated from a genetically manipulated source Details: Deletion mutation performed to remove flexible loop, removing residues 27-82. Numbering is correct in the pdb file. Source: (gene. exp.) ![]() ![]() ![]() Gene: Bcl2l1, Bcl2l, Bclx, BCL2L1, BCL2L, BCLX / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 2611.031 Da / Num. of mol.: 1 / Fragment: UNP residues 56-76 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 12% Peg 1500, 0.1M Sodium Acetate pH 5.5, 2.5M NaCl, 1.5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.99 Å / Num. obs: 11587 / % possible obs: 98.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.45→2.69 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 3.39 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FDL Resolution: 2.45→34.769 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→34.769 Å
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Refine LS restraints |
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LS refinement shell |
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