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Yorodumi- PDB-7ahz: Crystal structure of Western clawed frog MDM2 RING domain homodim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ahz | ||||||||||||
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Title | Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub | ||||||||||||
Components |
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Keywords | LIGASE / Ubiquitin ligase / RING E3 | ||||||||||||
Function / homology | Function and homology information Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Signaling by BMP / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Neddylation / Peroxisomal protein import / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / regulation of biological quality / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Signaling by BMP / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Neddylation / Peroxisomal protein import / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / regulation of biological quality / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K48-linked ubiquitination / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL Similarity search - Function | ||||||||||||
Biological species | Xenopus tropicalis (tropical clawed frog) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||||||||
Authors | Magnussen, H.M. / Huang, D.T. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Identification of a Catalytic Active but Non-Aggregating MDM2 RING Domain Variant. Authors: Magnussen, H.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 | 7ahz.cif.gz | 450.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ahz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ahz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/7ahz ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7ahz | HTTPS FTP |
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-Related structure data
Related structure data | 7ah2C 7ahyC 7ai0C 7ai1C 5mnjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
-Protein , 3 types, 12 molecules AAADDDGGGJJJBBBEEEHHHKKKCCCFFFIIILLL
#1: Protein | Mass: 7908.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: G412, S413: Expression tag. Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: mdm2, irak1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6P3Q9, RING-type E3 ubiquitin transferase #2: Protein | Mass: 16851.381 Da / Num. of mol.: 4 / Mutation: S22R, C85K Source method: isolated from a genetically manipulated source Details: C85K is covalently linked to G76 (Molecule 3). Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: ube2d3, ube2d2, TGas005e16.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28EY6 #3: Protein | Mass: 8922.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: G-4,S-3,G-2,G-1,S0: Expression tag G76 is covalently linked to C85K (Molecule 2). Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
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-Non-polymers , 3 types, 365 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 10 % w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→52.623 Å / Num. obs: 113701 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.82→1.85 Å / Num. unique obs: 5647 / CC1/2: 0.652 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MNJ Resolution: 1.82→52.623 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.044 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.125 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.798 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→52.623 Å
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Refine LS restraints |
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