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Yorodumi- PDB-5d1m: Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragmen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d1m | ||||||
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Title | Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A) | ||||||
Components |
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Keywords | LIGASE / ubiquitin conjugating enzyme (E2) / ubiquitin ligase (E3) / RING finger / ubiquitination / ubiquitin | ||||||
Function / homology | Function and homology information (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / NF-kappaB binding / protein autoubiquitination / protein K48-linked ubiquitination / cytosolic ribosome / ubiquitin ligase complex / rescue of stalled ribosome ...(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / NF-kappaB binding / protein autoubiquitination / protein K48-linked ubiquitination / cytosolic ribosome / ubiquitin ligase complex / rescue of stalled ribosome / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.581 Å | ||||||
Authors | Liang, Y.-H. / Li, S. / Weissman, A.M. / Ji, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B. Authors: Li, S. / Liang, Y.H. / Mariano, J. / Metzger, M.B. / Stringer, D.K. / Hristova, V.A. / Li, J. / Randazzo, P.A. / Tsai, Y.C. / Ji, X. / Weissman, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d1m.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d1m.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5d1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d1m_validation.pdf.gz | 469.7 KB | Display | wwPDB validaton report |
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Full document | 5d1m_full_validation.pdf.gz | 473.9 KB | Display | |
Data in XML | 5d1m_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 5d1m_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1m ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1m | HTTPS FTP |
-Related structure data
Related structure data | 5d1kSC 5d1lC 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 16755.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62837, ubiquitin-protein ligase |
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#2: Protein | Mass: 15571.507 Da / Num. of mol.: 1 / Fragment: UNP residues 126-258 / Mutation: P199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF25 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q96BH1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
-Non-polymers , 5 types, 381 molecules
#3: Chemical | ChemComp-OXL / | ||||
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#4: Chemical | ChemComp-PEG / | ||||
#5: Chemical | #6: Chemical | #7: 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: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2010 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→50 Å / Num. all: 39104 / Num. obs: 38987 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.22 Å2 / Rmerge(I) obs: 0.033 / Χ2: 1.097 / Net I/σ(I): 23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5D1K Resolution: 1.581→30.398 Å / Occupancy max: 1 / Occupancy min: 0.09 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.829 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.61 Å2 / Biso mean: 27.7522 Å2 / Biso min: 13.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.581→30.398 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: 7
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