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Yorodumi- PDB-7q16: Human 14-3-3 zeta fused to the BAD peptide including phosphoserine-74 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q16 | ||||||
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Title | Human 14-3-3 zeta fused to the BAD peptide including phosphoserine-74 | ||||||
Components | 14-3-3 protein zeta/delta,Bcl2-associated agonist of cell death | ||||||
Keywords | SIGNALING PROTEIN / apoptotic regulation / phosphorylation / phosphopeptide binding | ||||||
Function / homology | Function and homology information ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / positive regulation of glucokinase activity / BAD-BCL-2 complex / Golgi reassembly / glucose catabolic process / pore complex assembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus ...ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / positive regulation of glucokinase activity / BAD-BCL-2 complex / Golgi reassembly / glucose catabolic process / pore complex assembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / activation of cysteine-type endopeptidase activity / Rap1 signalling / cellular response to lipid / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to nucleus / regulation of mitochondrial membrane permeability / positive regulation of T cell differentiation / AKT phosphorylates targets in the cytosol / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of B cell differentiation / GP1b-IX-V activation signalling / NRAGE signals death through JNK / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of proteolysis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of localization of FOXO transcription factors / extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of autophagy / ATP metabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of TORC1 signaling / negative regulation of innate immune response / intrinsic apoptotic signaling pathway / regulation of ERK1 and ERK2 cascade / protein sequestering activity / release of cytochrome c from mitochondria / positive regulation of epithelial cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / phospholipid binding / positive regulation of insulin secretion / cytokine-mediated signaling pathway / cellular response to nicotine / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / melanosome / glucose homeostasis / cellular response to hypoxia / protein phosphatase binding / DNA-binding transcription factor binding / blood microparticle / vesicle / mitochondrial outer membrane / transmembrane transporter binding / cadherin binding / positive regulation of apoptotic process / protein phosphorylation / focal adhesion / lipid binding / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å | ||||||
Authors | Sluchanko, N.N. / Tugaeva, K.V. / Gushchin, I. / Remeeva, A. / Kovalev, K. / Cooley, R.B. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Crystal structure of human 14-3-3 zeta complexed with the noncanonical phosphopeptide from proapoptotic BAD. Authors: Sluchanko, N.N. / Tugaeva, K.V. / Gushchin, I. / Remeeva, A. / Kovalev, K. / Cooley, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q16.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q16.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 7q16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/7q16 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q16 | HTTPS FTP |
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-Related structure data
Related structure data | 6zfdS S: Starting model for refinement |
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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: 27552.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ, BAD, BBC6, BCL2L8 / Production host: Escherichia coli (E. coli) / References: UniProt: P63104, UniProt: Q92934 |
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#2: 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: 3.3 Å3/Da / Density % sol: 62.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4 % w/v PEG 8000, 20 % v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.356→45.062 Å / Num. obs: 11472 / % possible obs: 93.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 52.49 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.356→2.523 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 574 / CC1/2: 0.523 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZFD Resolution: 2.356→45.062 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.96 / 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: 148.3 Å2 / Biso mean: 60.2522 Å2 / Biso min: 29.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.356→45.062 Å
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Refine LS restraints |
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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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