+Open data
-Basic information
Entry | Database: PDB / ID: 3oj4 | ||||||
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Title | Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex | ||||||
Components |
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Keywords | LIGASE/PROTEIN BINDING / ubiquitin / zinc finger / ubiquitin conjugating enzyme / zinc ion / LIGASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / positive regulation of protein polyubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of chronic inflammatory response / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / negative regulation of toll-like receptor 4 signaling pathway / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of germinal center formation / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K48-linked deubiquitination / B-1 B cell homeostasis / Phosphorylation of the APC/C / Signaling by BMP / regulation of defense response to virus by host / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of bone resorption / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / fat pad development / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / E2 ubiquitin-conjugating enzyme / female gonad development / negative regulation of NF-kappaB transcription factor activity / seminiferous tubule development / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of interleukin-6 production / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / response to muramyl dipeptide / negative regulation of BMP signaling pathway / negative regulation of tumor necrosis factor production / Transcriptional Regulation by VENTX / positive regulation of Wnt signaling pathway / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / negative regulation of protein ubiquitination / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / negative regulation of TORC1 signaling / 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 / cytoskeleton organization / 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 / 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 / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Bosanac, I. / Hymowitz, S.G. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling Authors: Bosanac, I. / Wertz, I.E. / Pan, B. / Yu, C. / Kusam, S. / Lam, C. / Phu, L. / Phung, Q. / Maurer, B. / Arnott, D. / Kirkpatrick, D.S. / Dixit, V.M. / Hymowitz, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oj4.cif.gz | 219.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oj4.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 3oj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3oj4 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3oj4 | HTTPS FTP |
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-Related structure data
Related structure data | 3oj3C 1ubqS 1x23S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 17277.756 Da / Num. of mol.: 2 / Fragment: Ubiquitin-conjugating enzyme E2 D1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P51668, ubiquitin-protein ligase #2: Protein | Mass: 8859.106 Da / Num. of mol.: 2 / Fragment: Ubiquitin, UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P0CG47, UniProt: P0CG48*PLUS #3: Protein/peptide | Mass: 5418.088 Da / Num. of mol.: 2 / Fragment: Zinc finger A20-type 4, UNP residues 592-635 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3, OTUD7C / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P21580 #4: Chemical | |
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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: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.1 Details: 0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2006 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→25 Å / Num. all: 9814 / Num. obs: 9637 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.115 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 955 / Rsym value: 0.75 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 1UBQ, 1X23 Resolution: 3.4→25 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.842 / SU B: 102.112 / SU ML: 0.724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.767 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.095 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.4→3.469 Å / Rfactor Rfree error: 43.6 / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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