+Open data
-Basic information
Entry | Database: PDB / ID: 8ivb | ||||||
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Title | K113-Ubiquitinated BAK | ||||||
Components |
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Keywords | APOPTOSIS / pro-apoptotic BCL-2 proteins | ||||||
Function / homology | Function and homology information Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / Formation of the ternary complex, and subsequently, the 43S complex / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of proteolysis / Selenocysteine synthesis / positive regulation of IRE1-mediated unfolded protein response / Formation of a pool of free 40S subunits / positive regulation of release of cytochrome c from mitochondria / Eukaryotic Translation Termination / vagina development / B cell homeostasis / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Major pathway of rRNA processing in the nucleolus and cytosol / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of peptidyl-serine phosphorylation / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / heat shock protein binding / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Dong, X. / Cheng, P. / Hou, Y.Z. / Chen, Y.K. / Liu, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Parkin-mediated ubiquitination inhibits BAK apoptotic activity by blocking its canonical hydrophobic groove. Authors: Cheng, P. / Hou, Y. / Bian, M. / Fang, X. / Liu, Y. / Rao, Y. / Cao, S. / Liu, Y. / Zhang, S. / Chen, Y. / Dong, X. / Liu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ivb.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8ivb.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8ivb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/8ivb ftp://data.pdbj.org/pub/pdb/validation_reports/iv/8ivb | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8622.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979 |
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#2: Protein | Mass: 18924.205 Da / Num. of mol.: 1 / Mutation: K113C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 20 mM sodium phosphate, 0.1 M sodium chloride, 95% H2O/5% D2O Label: 13C15N sample / Solvent system: 95% H2O/5% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: condition1 / pH: 6.8 / Pressure: 1 bar / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CcpNmr Analysis / Developer: CCPN / Classification: chemical shift assignment |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 240 / Conformers submitted total number: 20 |