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Yorodumi- PDB-6sqs: Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sqs | |||||||||
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Title | Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub | |||||||||
Components |
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Keywords | LIGASE / MDM2 / MDMX / E3 / E2 / ubiquitin ligase / ubiquitin / phosphorylation | |||||||||
Function / homology | Function and homology information regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / E2 ubiquitin-conjugating enzyme / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...regulation of biological quality / (E3-independent) E2 ubiquitin-conjugating enzyme / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / E2 ubiquitin-conjugating enzyme / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin conjugating enzyme activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein autoubiquitination / protein K48-linked ubiquitination / cytosolic ribosome / ribonucleoprotein complex binding / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL Similarity search - Function | |||||||||
Biological species | Felis catus (domestic cat) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | |||||||||
Authors | Magnussen, H.M. / Ahmed, S.F. / Huang, D.T. | |||||||||
Funding support | United Kingdom, Belgium, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for DNA damage-induced phosphoregulation of MDM2 RING domain. Authors: Magnussen, H.M. / Ahmed, S.F. / Sibbet, G.J. / Hristova, V.A. / Nomura, K. / Hock, A.K. / Archibald, L.J. / Jamieson, A.G. / Fushman, D. / Vousden, K.H. / Weissman, A.M. / Huang, D.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sqs.cif.gz | 129.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sqs.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 6sqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sqs_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 6sqs_full_validation.pdf.gz | 421.6 KB | Display | |
Data in XML | 6sqs_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6sqs_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/6sqs ftp://data.pdbj.org/pub/pdb/validation_reports/sq/6sqs | HTTPS FTP |
-Related structure data
Related structure data | 6sqoC 6sqpC 6sqrC 5mnjS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 7287.754 Da / Num. of mol.: 2 / Mutation: G443T Source method: isolated from a genetically manipulated source Details: Residues 422-491 and contains G443T mutation. S429 is phosphorylated. GS at the N-terminus resulted from cloning. Source: (gene. exp.) Felis catus (domestic cat) / Gene: MDM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q7YRZ8, RING-type E3 ubiquitin transferase #2: Protein | Mass: 16720.186 Da / Num. of mol.: 2 / Mutation: S22R, C85K Source method: isolated from a genetically manipulated source Details: Contains S22R and C85K mutations. K85 in Chains B and E form a covalent bond with G76 in Chains C and F, respectively. Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli) References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme #3: Protein | Mass: 8663.908 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Contains a GSGGS at the N-terminus resulted from cloning. G76 in Chains C and F form a covalent bond with K85 sidechain in Chains B and E, respectively. Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli (E. coli) / References: UniProt: J3QTR3, UniProt: P62979*PLUS #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 0.1 M Tris-HCl, pH 8.0, 15% (w/v) PEG 2000 MME and 0.1 M KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2018 |
Radiation | Monochromator: 0.916 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→29.2 Å / Num. obs: 49057 / % possible obs: 95.8 % / Redundancy: 1.8 % / CC1/2: 0.996 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.83→1.88 Å / Num. unique obs: 3293 / CC1/2: 0.539 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MNJ Resolution: 1.83→29.2 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.83→29.2 Å
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