+Open data
-Basic information
Entry | Database: PDB / ID: 2xa0 | ||||||
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Title | Crystal structure of BCL-2 in complex with a BAX BH3 peptide | ||||||
Components |
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Keywords | APOPTOSIS / CELL DEATH | ||||||
Function / homology | Function and homology information outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation ...outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / inner mitochondrial membrane organization / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of glycoprotein biosynthetic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of B cell apoptotic process / positive regulation of melanocyte differentiation / development of secondary sexual characteristics / myeloid cell apoptotic process / Sertoli cell proliferation / osteoblast proliferation / positive regulation of apoptotic DNA fragmentation / cochlear nucleus development / B cell homeostatic proliferation / mesenchymal cell development / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / positive regulation of neuron maturation / BH domain binding / negative regulation of osteoblast proliferation / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / sex differentiation / limb morphogenesis / gland morphogenesis / renal system process / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / post-embryonic camera-type eye morphogenesis / negative regulation of calcium ion transport into cytosol / The NLRP1 inflammasome / dendritic cell apoptotic process / melanocyte differentiation / ear development / lymphoid progenitor cell differentiation / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / glomerulus development / B cell apoptotic process / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / neuron maturation / metanephros development / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / negative regulation of B cell apoptotic process / negative regulation of ossification / response to UV-B / response to iron ion / cellular respiration / regulation of mitochondrial membrane permeability / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / negative regulation of mitochondrial depolarization / regulation of mitochondrial membrane permeability involved in apoptotic process / motor neuron apoptotic process / mitochondrial fusion / channel activity / axon regeneration Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ku, B. / Oh, B.H. | ||||||
Citation | Journal: Cell Res. / Year: 2011 Title: Evidence that Inhibition of Bax Activation by Bcl- 2 Involves its Tight and Preferential Interaction with the Bh3 Domain of Bax. Authors: Ku, B. / Liang, C. / Jung, J.U. / Oh, B.H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xa0.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xa0.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xa0 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xa0 | HTTPS FTP |
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-Related structure data
Related structure data | 1g5mS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22861.713 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIG / References: UniProt: P10415 #2: Protein/peptide | Mass: 3572.035 Da / Num. of mol.: 2 / Fragment: BH3 DOMAIN, RESIDUES 52-82 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q07813 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.23 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE (PH 4.2), 3.0 M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 14540 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.5 / % possible all: 75.3 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G5M Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: RESIDUES 35-50 OF BCL-2 ARE REPLACED WITH RESIDUES 33-48 OF BCL-XL TO SOLUBILIZE THE PROTEIN AS REPORTED EARLIER (PETROS ET AL, PROC NATL ACAD SCI U S A 98, 3012-3017(2001)) . HOWEVER, THE ...Details: RESIDUES 35-50 OF BCL-2 ARE REPLACED WITH RESIDUES 33-48 OF BCL-XL TO SOLUBILIZE THE PROTEIN AS REPORTED EARLIER (PETROS ET AL, PROC NATL ACAD SCI U S A 98, 3012-3017(2001)) . HOWEVER, THE FINAL MODEL DOES NOT INCLUDE THE ENTIRE BCL- XL SUBSTITUTION REGION, WHOSE ELECTRON DENSITIES WERE NOT OBSERVED.
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Solvent computation | Bsol: 44.8143 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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