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Yorodumi- PDB-2a4d: Structure of the human ubiquitin-conjugating enzyme E2 variant 1 ... -
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-Basic information
Entry | Database: PDB / ID: 2a4d | ||||||
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Title | Structure of the human ubiquitin-conjugating enzyme E2 variant 1 (UEV-1) | ||||||
Components | Ubiquitin-conjugating enzyme E2 variant 1 | ||||||
Keywords | LIGASE / Alternative splicing / Nuclear protein / Ubl conjugation pathway / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information : / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation ...: / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol Cell Proteomics / Year: 2012 Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a4d.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a4d.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a4d ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a4d | HTTPS FTP |
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-Related structure data
Related structure data | 1y6lC 1yh2C 1yrvC 1zdnC 1zuoC 2a7lC 2awfC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC 3cegC 1j7dS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a monomer. |
-Components
#1: Protein | Mass: 18027.576 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 82-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V1, CROC1, UBE2V, UEV1 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13404, ubiquitin-protein ligase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.06 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 32% PEG1500, 0.2 M NaCl, 1 mM DTT, 0.1 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→30 Å / Num. obs: 13994 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 44 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J7D Resolution: 1.69→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.764 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.124 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.74 Å / Total num. of bins used: 20
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