+Open data
-Basic information
Entry | Database: PDB / ID: 5tdd | ||||||
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Title | Human UBR-box from UBR2 in complex with HIFS peptide | ||||||
Components |
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Keywords | LIGASE / UBR-box / N-end rule / Zinc finger / N-degron | ||||||
Function / homology | Function and homology information L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / histone ubiquitin ligase activity / male meiotic nuclear division / retrotransposon silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / male meiosis I / ubiquitin ligase complex ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / histone ubiquitin ligase activity / male meiotic nuclear division / retrotransposon silencing / cellular response to L-leucine / negative regulation of TOR signaling / reciprocal meiotic recombination / male meiosis I / ubiquitin ligase complex / heterochromatin formation / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / spermatogenesis / protein ubiquitination / chromatin / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Munoz-Escobar, J. / Kozlov, G. / Gehring, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2017 Title: Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase. Authors: Munoz-Escobar, J. / Matta-Camacho, E. / Cho, C. / Kozlov, G. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tdd.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tdd.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 5tdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/5tdd ftp://data.pdbj.org/pub/pdb/validation_reports/td/5tdd | HTTPS FTP |
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-Related structure data
Related structure data | 5tdaC 5tdbC 5tdcC 5um3C 3ny3S 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: 8350.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBR2, C6orf133, KIAA0349 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q8IWV8, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
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#2: Protein/peptide | Mass: 503.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | #4: Chemical | #5: 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: 1.8 Å3/Da / Density % sol: 30 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6362 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6362 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20.727 Å / Num. obs: 9083 / % possible obs: 99.94 % / Redundancy: 6.4 % / Rsym value: 0.1 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 4.8 / CC1/2: 0.851 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NY3 Resolution: 1.55→20.727 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20.727 Å
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Refine LS restraints |
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LS refinement shell |
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