+Open data
-Basic information
Entry | Database: PDB / ID: 8hlm | ||||||
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Title | Crystal structure of p53/BCL2 fusion complex (complex 2) | ||||||
Components |
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Keywords | APOPTOSIS | ||||||
Function / homology | Function and homology information 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 / positive regulation of melanocyte differentiation / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / positive regulation of skeletal muscle fiber development / melanin metabolic process ...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 / positive regulation of melanocyte differentiation / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / positive regulation of skeletal muscle fiber development / melanin metabolic process / myeloid cell apoptotic process / gland morphogenesis / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / ear development / lymphoid progenitor cell differentiation / melanocyte differentiation / renal system process / stem cell development / regulation of cell-matrix adhesion / negative regulation of calcium ion transport into cytosol / The NLRP1 inflammasome / dendritic cell apoptotic process / : / T cell apoptotic process / B cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / regulation of nitrogen utilization / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / Regulation of MITF-M-dependent genes involved in apoptosis / neuron maturation / positive regulation of multicellular organism growth / focal adhesion assembly / metanephros development / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / regulation of mitochondrial membrane permeability / negative regulation of ossification / calcium ion transport into cytosol / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of B cell apoptotic process / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / regulation of fibroblast apoptotic process / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / response to UV-B / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / response to iron ion / circadian behavior / mRNA transcription / bone marrow development / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / germ cell nucleus / T cell lineage commitment / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / axon regeneration / organ growth / TP53 Regulates Transcription of Death Receptors and Ligands / BH domain binding / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / hair follicle morphogenesis / smooth muscle cell migration / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / B cell lineage commitment / thymocyte apoptotic process / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.522 Å | ||||||
Authors | Guo, M. / Wang, H. / Wei, H. / Chen, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity. Authors: Wei, H. / Wang, H. / Wang, G. / Qu, L. / Jiang, L. / Dai, S. / Chen, X. / Zhang, Y. / Chen, Z. / Li, Y. / Guo, M. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hlm.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hlm.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 8hlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hlm_validation.pdf.gz | 829.7 KB | Display | wwPDB validaton report |
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Full document | 8hlm_full_validation.pdf.gz | 831.6 KB | Display | |
Data in XML | 8hlm_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 8hlm_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/8hlm ftp://data.pdbj.org/pub/pdb/validation_reports/hl/8hlm | HTTPS FTP |
-Related structure data
Related structure data | 8hllC 8hlnC 1tupS 6qggS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22103.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637 |
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#2: Protein | Mass: 19502.291 Da / Num. of mol.: 1 Mutation: H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M Imidazole, PEG8K 15-21% / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→63.58 Å / Num. obs: 13872 / % possible obs: 96.21 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08788 / Net I/σ(I): 0.0935 |
Reflection shell | Resolution: 2.522→2.612 Å / Rmerge(I) obs: 0.9106 / Num. unique obs: 1383 / CC1/2: 0.924 / CC star: 0.98 / Rpim(I) all: 0.3083 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TUP/6QGG Resolution: 2.522→27.205 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.93 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 180.68 Å2 / Biso mean: 87.9855 Å2 / Biso min: 47.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.522→27.205 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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