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Yorodumi- PDB-1g3f: NMR STRUCTURE OF A 9 RESIDUE PEPTIDE FROM SMAC/DIABLO COMPLEXED T... -
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-Basic information
Entry | Database: PDB / ID: 1g3f | ||||||
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Title | NMR STRUCTURE OF A 9 RESIDUE PEPTIDE FROM SMAC/DIABLO COMPLEXED TO THE BIR3 DOMAIN OF XIAP | ||||||
Components |
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Keywords | APOPTOSIS / zinc finger / complex / peptide-protein / BIR | ||||||
Function / homology | Function and homology information endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / Release of apoptotic factors from the mitochondria / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / Release of apoptotic factors from the mitochondria / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / CD40 receptor complex / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / intrinsic apoptotic signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / positive regulation of apoptotic process / apoptotic process / DNA damage response / negative regulation of apoptotic process / mitochondrion / nucleoplasm / metal ion binding / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Liu, Z. / Sun, C. / Olejniczak, E.T. / Meadows, R.P. / Betz, S.F. / Oost, T. / Herrmann, J. / Wu, J.C. / Fesik, S.W. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain. Authors: Liu, Z. / Sun, C. / Olejniczak, E.T. / Meadows, R.P. / Betz, S.F. / Oost, T. / Herrmann, J. / Wu, J.C. / Fesik, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3f.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3f.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1g3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3f ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13424.951 Da / Num. of mol.: 1 / Fragment: RESIDUES 241-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P98170 |
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#2: Protein/peptide | Mass: 943.074 Da / Num. of mol.: 1 / Fragment: 9 RESIDUE PEPTIDE / Source method: obtained synthetically / Details: The 9 residue peptide was chemically synthesized. / References: UniProt: Q9NR28 |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 15N-separated NOESY |
-Sample preparation
Details | Contents: 1 mM protein/peptide complex, 120 mM NaCl, 1mM DTT, 10mM phosphate Solvent system: 90% h20, 10% d20 |
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Sample conditions | pH: 7.2 / Pressure: 1 atm / Temperature: 300 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
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-Processing
NMR software | Name: CNX / Version: 2000 / Developer: brunger / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: minimized average structure |
NMR ensemble | Conformers submitted total number: 1 |