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Yorodumi- PDB-7m4o: Crystal structure of phosphorylated RBR E3 ligase RNF216 in compl... -
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-Basic information
Entry | Database: PDB / ID: 7m4o | ||||||
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Title | Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin | ||||||
Components |
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Keywords | LIGASE / E3 ligase / RBR / ubiquitin / enzyme | ||||||
Function / homology | Function and homology information regulation of interferon-beta production / protein linear polyubiquitination / LUBAC complex / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...regulation of interferon-beta production / protein linear polyubiquitination / LUBAC complex / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / protein K48-linked ubiquitination / 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 / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Cotton, T.R. / Lechtenberg, B.C. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Mol.Cell / Year: 2022 Title: Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Authors: Cotton, T.R. / Cobbold, S.A. / Bernardini, J.P. / Richardson, L.W. / Wang, X.S. / Lechtenberg, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m4o.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m4o.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 7m4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m4o_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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Full document | 7m4o_full_validation.pdf.gz | 470.1 KB | Display | |
Data in XML | 7m4o_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7m4o_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/7m4o ftp://data.pdbj.org/pub/pdb/validation_reports/m4/7m4o | HTTPS FTP |
-Related structure data
Related structure data | 7m4mC 7m4nSC 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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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 15853.939 Da / Num. of mol.: 1 / Mutation: C688A Source method: isolated from a genetically manipulated source Details: Serine 719 is phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: RNF216, TRIAD3, UBCE7IP1, ZIN / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9NWF9, RING-type E3 ubiquitin transferase |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: K63-linked di-ubiquitin; C-terminus of chain B conjugated to Lys63 of chain C via an isopeptide bond. Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48 |
-Non-polymers , 5 types, 91 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PG0 / | #7: 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: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.22 Details: 0.259 M ammonium sulfate, 30.1 % PEG monomethyl ether 2000, 0.1M sodium acetate-acetic acid pH 5.22 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→45.05 Å / Num. obs: 16539 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.08 / Rrim(I) all: 0.154 / Χ2: 0.54 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1375 / CC1/2: 0.793 / Rpim(I) all: 0.594 / Rrim(I) all: 1.132 / Χ2: 0.48 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7M4N Resolution: 2.21→45.05 Å / SU ML: 0.3032 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.9422 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→45.05 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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