+Open data
-Basic information
Entry | Database: PDB / ID: 8b5w | ||||||
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Title | Crystal structure of the E3 module from UBR4 | ||||||
Components | cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA | ||||||
Keywords | LIGASE / ubiquitin / E3 ligase / zinc finger | ||||||
Function / homology | E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / ligase activity / cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Virdee, S. / Mabbitt, P.D. / Barnsby-Greer, L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4. Authors: Barnsby-Greer, L. / Mabbitt, P.D. / Dery, M.A. / Squair, D.R. / Wood, N.T. / Lamoliatte, F. / Lange, S.M. / Virdee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b5w.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b5w.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 8b5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b5w_validation.pdf.gz | 851.2 KB | Display | wwPDB validaton report |
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Full document | 8b5w_full_validation.pdf.gz | 852.2 KB | Display | |
Data in XML | 8b5w_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 8b5w_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b5w ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b5w | HTTPS FTP |
-Related structure data
Related structure data | 8btlC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51755.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B3KMT2 | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10 mM Na2HPO4 13% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.2820 or 1.2831 | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2019 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→74.07 Å / Num. obs: 36081 / % possible obs: 91.33 % / Redundancy: 2 % / Biso Wilson estimate: 24.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02395 / Rpim(I) all: 0.02395 / Rrim(I) all: 0.03387 / Net I/σ(I): 23.84 | |||||||||
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2907 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 3577 / CC1/2: 0.872 / CC star: 0.965 / Rpim(I) all: 0.2907 / Rrim(I) all: 0.4111 / % possible all: 91.67 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→74.07 Å / SU ML: 0.2153 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3732 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 28.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→74.07 Å
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Refine LS restraints |
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LS refinement shell |
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