+Open data
-Basic information
Entry | Database: PDB / ID: 4nri | ||||||
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Title | Crystal Structure of a human Mms2/Ubc13 A122G mutant | ||||||
Components |
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Keywords | LIGASE / ubc13 / mms2 / E2 / ubiquitin conjugating enzyme | ||||||
Function / homology | Function and homology information error-free postreplication DNA repair / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction ...error-free postreplication DNA repair / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / regulation of DNA repair / ubiquitin ligase complex / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of DNA repair / 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 / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Hodge, C.D. / Edwards, R.A. / Glover, J.N.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes. Authors: Rout, M.K. / Hodge, C.D. / Markin, C.J. / Xu, X. / Glover, J.N. / Xiao, W. / Spyracopoulos, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nri.cif.gz | 131.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nri.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/4nri ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nri | HTTPS FTP |
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-Related structure data
Related structure data | 4nr3C 4nrgC 1j7dS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16676.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMS2, UBE2V2, UEV2 / Plasmid: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q15819 |
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#2: Protein | Mass: 17499.066 Da / Num. of mol.: 1 / Mutation: A122G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Plasmid: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P61088, ubiquitin-protein ligase |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 4, 2013 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. all: 14213 / Num. obs: 14213 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.78 Å2 / Rmerge(I) obs: 0.149 / Χ2: 1.016 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1J7D Resolution: 2.3→25.095 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8431 / SU ML: 0.27 / σ(F): 1.38 / Phase error: 22.1 / Stereochemistry target values: ML
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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 max: 140.45 Å2 / Biso mean: 36.1541 Å2 / Biso min: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25.095 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 23.5654 Å / Origin y: 23.6888 Å / Origin z: 22.9088 Å
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Refinement TLS group |
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