+Open data
-Basic information
Entry | Database: PDB / ID: 4v3k | ||||||
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Title | RNF38-UbcH5B-UB complex | ||||||
Components |
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Keywords | LIGASE / RING E3 / E2 / UBIQUITIN | ||||||
Function / homology | Function and homology information (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein K48-linked ubiquitination / protein autoubiquitination / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / 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 / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / 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 / Negative regulation of FGFR3 signaling / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Buetow, L. / Gabrielsen, M. / Anthony, N.G. / Dou, H. / Patel, A. / Aitkenhead, H. / Sibbet, G.J. / Smith, B.O. / Huang, D.T. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Activation of a Primed Ring E3-E2-Ubiquitin Complex by Non-Covalent Ubiquitin. Authors: Buetow, L. / Gabrielsen, M. / Anthony, N.G. / Dou, H. / Patel, A. / Aitkenhead, H. / Sibbet, G.J. / Smith, B.O. / 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 | 4v3k.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3k.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 4v3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v3k_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 4v3k_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 4v3k_validation.xml.gz | 27 KB | Display | |
Data in CIF | 4v3k_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3k ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3k | HTTPS FTP |
-Related structure data
Related structure data | 4v3lC 1x4jS 3zniS 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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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 16720.186 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-147 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase #2: Protein | Mass: 8922.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 77-152 Source method: isolated from a genetically manipulated source Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48 #3: Protein | Mass: 9135.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 439-515 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0F5, ubiquitin-protein ligase |
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-Non-polymers , 4 types, 383 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ZN / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION. SER22 IS MUTATED TO ARGININE. CYS85 IS ...N-TERMINAL METHIONINE |
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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: 2.48 Å3/Da / Density % sol: 50.33 % / Description: NONE |
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Crystal grow | Details: 50 MM TRIS-HCL, PH 8.5 AND 2.3 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→34.9 Å / Num. obs: 44936 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3ZNI AND 1X4J Resolution: 2.04→34.905 Å / SU ML: 0.63 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML Details: IN CHAIN C, RESIDUES 389 AND 465 ARE DISORDERED. IN CHAIN F, RESIDUE 389 AND 460-465 ARE DISORDERED. RESIDUES WITH POOR SIDE CHAIN ELECTRON DENSITY WERE BUILT AS ALANINE.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.741 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→34.905 Å
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Refine LS restraints |
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LS refinement shell |
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