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- PDB-6sqo: Crystal structure of human MDM2 RING domain homodimer bound to Ub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sqo | |||||||||
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Title | Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub | |||||||||
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![]() | LIGASE / Ubiquitin ligase / E3 / MDM2 / MDMX / E2 / phosphorylation / p53 | |||||||||
Function / homology | ![]() cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / (E3-independent) E2 ubiquitin-conjugating enzyme / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / (E3-independent) E2 ubiquitin-conjugating enzyme / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to iron ion / response to steroid hormone / NEDD8 ligase activity / Formation of the ternary complex, and subsequently, the 43S complex / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / Translation initiation complex formation / Ribosomal scanning and start codon recognition / endocardial cushion morphogenesis / E2 ubiquitin-conjugating enzyme / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / ligase activity / Selenocysteine synthesis / negative regulation of DNA damage response, signal transduction by p53 class mediator / ubiquitin conjugating enzyme activity / Formation of a pool of free 40S subunits / response to magnesium ion / Eukaryotic Translation Termination / SUMOylation of transcription factors / Response of EIF2AK4 (GCN2) to amino acid deficiency / protein sumoylation / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to UV-C / Major pathway of rRNA processing in the nucleolus and cytosol / blood vessel remodeling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cellular response to estrogen stimulus / protein autoubiquitination / protein K48-linked ubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / cytosolic ribosome / 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 / positive regulation of vascular associated smooth muscle cell proliferation / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NPAS4 regulates expression of target genes / 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 / transcription repressor complex / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Magnussen, H.M. / Ahmed, S.F. / Huang, D.T. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 214.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 454.7 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sqpC ![]() 6sqrC ![]() 6sqsC ![]() 5mnjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 6920.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Construct contains MDM2 residues 419-491. Residues 419-427 are absent due to lack of electron density. GS at the N-terminus resulted from cloning. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q00987, 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: K85 sidechains from Chains B and E form an isopeptide bond with the C-terminus of G76 in Chains C and F, respectively. Source: (gene. exp.) ![]() ![]() ![]() 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: GSGGS LINKER AT THE N-TERMINUS RESULTED FROM CLONING. G76 IN CHAINS C and F ARE COVALENTLY LINKED TO K85 SIDE CHAIN IN CHAINS B AND E, RESPECTIVELY. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 556 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NO3.gif)
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#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 0.1 M SPG, pH 7.0, 10% (w/v) PEG Smear Broad, 0.15 M NH4NO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→112 Å / Num. obs: 129794 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 6423 / CC1/2: 0.542 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MNJ Resolution: 1.41→112 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.41→112 Å
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