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- PDB-3m63: Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m63 | ||||||
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Title | Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 | ||||||
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![]() | LIGASE/PROTEIN BINDING / Armadillo-like repeats / Ubl conjugation pathway / Nucleus / Phosphoprotein / LIGASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / ubiquitin-ubiquitin ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / positive regulation of protein ubiquitination ...Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / ubiquitin-ubiquitin ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / protein K48-linked ubiquitination / ERAD pathway / ubiquitin ligase complex / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Haenzelmann, P. / Schindelin, H. | ||||||
![]() | ![]() Title: The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. Authors: Hanzelmann, P. / Stingele, J. / Hofmann, K. / Schindelin, H. / Raasi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.6 KB | Display | ![]() |
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PDB format | ![]() | 175.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.8 KB | Display | ![]() |
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Full document | ![]() | 483.7 KB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m62C ![]() 2qizS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 110806.328 Da / Num. of mol.: 1 / Mutation: S102L, D677V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: D1255, UFD2, YDL190C / Production host: ![]() ![]() |
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#2: Protein | Mass: 11539.952 Da / Num. of mol.: 1 / Fragment: UNP residues 1-75, Ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DSK2, SHE4, YM8021.02, YMR276W / Production host: ![]() ![]() |
#3: Chemical | ChemComp-1PE / |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→73.501 Å / Num. all: 58089 / Num. obs: 58089 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.2 / Num. unique all: 58089 / Rsym value: 0.509 / % possible all: 95.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QIZ Resolution: 2.4→73.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 19.187 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.321 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.92 Å2 / Biso mean: 42.881 Å2 / Biso min: 12.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→73.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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