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Yorodumi- PDB-4gof: Crystal structure of the SGTA homodimerization domain with covale... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gof | ||||||
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Title | Crystal structure of the SGTA homodimerization domain with covalent modifications to both C38 | ||||||
Components | Small glutamine-rich tetratricopeptide repeat-containing protein alpha | ||||||
Keywords | PROTEIN BINDING / Four-helix bundle / Protein-protein interaction / Ubl4A ubiquitin-like domain | ||||||
Function / homology | Function and homology information TRC complex / negative regulation of ERAD pathway / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ERAD pathway / negative regulation of ubiquitin-dependent protein catabolic process ...TRC complex / negative regulation of ERAD pathway / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ERAD pathway / negative regulation of ubiquitin-dependent protein catabolic process / : / molecular adaptor activity / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Chartron, J.W. / VanderVelde, D.G. / Clemons Jr., W.M. | ||||||
Citation | Journal: Cell Rep / Year: 2012 Title: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface. Authors: Chartron, J.W. / Vandervelde, D.G. / Clemons, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gof.cif.gz | 29.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gof.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 4gof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4gof ftp://data.pdbj.org/pub/pdb/validation_reports/go/4gof | HTTPS FTP |
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-Related structure data
Related structure data | 2lxaC 2lxbC 2lxcC 4gocC 4godC 4goeC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 5738.505 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SGT, SGT1, SGTA / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: O43765 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 1.78 Å3/Da / Density % sol: 31.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10% 2-propanol, 0.1 M sodium citrate, 26% PEG 400, 10 mM 2-mercaptoethanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2012 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→19.39 Å / Num. obs: 18421 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.7 / Num. unique all: 876 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.39 Å / SU ML: 0.13 / σ(F): 1.77 / Phase error: 18.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→19.39 Å
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Refine LS restraints |
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LS refinement shell |
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