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Open data
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Basic information
Entry | Database: PDB / ID: 9dno | |||||||||||||||
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Title | Structure of UBR1-RFF complex | |||||||||||||||
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![]() | PROTEIN BINDING / UBR / E3 ligase / natural ligands | |||||||||||||||
Function / homology | ![]() L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process ...L-leucine binding / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cellular response to L-leucine / negative regulation of TOR signaling / ubiquitin ligase complex / proteasome complex / RING-type E3 ubiquitin transferase / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Huang, S. / Wu, J. / Taylor, S. / Chen, Y. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Flexibility and Selectivity of N-End Rule Ligases Authors: Huang, S.T. / Wu, J. / Taylor, S. / Chen, Y. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.2 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9dnpC ![]() 9dnqC ![]() 9dnrC ![]() 9muxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8449.517 Da / Num. of mol.: 2 / Fragment: UBR-box domain (UNP residues 97-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): Amp resistance, N-terminal GST tag Production host: ![]() ![]() #2: Protein/peptide | Mass: 467.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 36.46 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: The stock concentration of UBR1UBR for co-crystallization is 7.52 mg/ml. The ligand to protein molar ratio for UBR1UBR-RFF co-crystal is 1:2, and the reservoir contains 0.1 M Bis-Tris pH 5.5 ...Details: The stock concentration of UBR1UBR for co-crystallization is 7.52 mg/ml. The ligand to protein molar ratio for UBR1UBR-RFF co-crystal is 1:2, and the reservoir contains 0.1 M Bis-Tris pH 5.5 with 24% PEG 3350. Crystals were soaked in cryoprotection liquid consisting of mother reservoir condition supplemented with 15% glycerol prior to flash freezing in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→48.97 Å / Num. obs: 36357 / % possible obs: 91.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.59 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.23→1.25 Å / Mean I/σ(I) obs: 0.1 / Num. unique obs: 909 / CC1/2: 0.053 / % possible all: 45.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→47.8 Å
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Refine LS restraints |
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LS refinement shell |
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