+Open data
-Basic information
Entry | Database: PDB / ID: 1zx2 | ||||||
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Title | Crystal Structure of Yeast UBP3-associated Protein BRE5 | ||||||
Components | UBP3-associated protein BRE5 | ||||||
Keywords | SIGNALING PROTEIN / Ubp3 / deubiqutinate / NTF2 | ||||||
Function / homology | Function and homology information Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / regulation of ER to Golgi vesicle-mediated transport / protein retention in Golgi apparatus / negative regulation of mitophagy / protein deubiquitination / stress granule assembly / P-body / ribonucleoprotein complex ...Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / regulation of ER to Golgi vesicle-mediated transport / protein retention in Golgi apparatus / negative regulation of mitophagy / protein deubiquitination / stress granule assembly / P-body / ribonucleoprotein complex / mRNA binding / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Li, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural basis for interaction between the Ubp3 deubiquitinating enzyme and its Bre5 cofactor Authors: Li, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R. #1: Journal: Nat.Cell Biol. / Year: 2003 Title: Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23 Authors: Cohen, M. / Stutz, F. / Belgareh, N. / Haguenauer-Tsapis, R. / Dargemont, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zx2.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zx2.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1zx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zx2_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 1zx2_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1zx2_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1zx2_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zx2 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zx2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 16948.256 Da / Num. of mol.: 2 / Fragment: NTF2-like domains (residues 1-146) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BRE5 / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53741 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 3350, Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795, 0.9794, 0.9500, 0.9790 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2004 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 28566 / % possible obs: 99.2 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.3 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 8.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→79.06 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.883 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→79.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.097→2.152 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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