+Open data
-Basic information
Entry | Database: PDB / ID: 2vyi | ||||||
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Title | Crystal Structure of the TPR domain of Human SGT | ||||||
Components | SGTA PROTEIN | ||||||
Keywords | CHAPERONE / SGT / TPR REPEAT / PHOSPHOPROTEIN / TETRATRICOPEPTIDE REPEAT PROTEIN / HOST-VIRUS INTERACTION | ||||||
Function / homology | Function and homology information : / positive regulation of chaperone-mediated protein folding / : / TRC complex / negative regulation of ERAD pathway / : / : / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / extrinsic component of synaptic vesicle membrane ...: / positive regulation of chaperone-mediated protein folding / : / TRC complex / negative regulation of ERAD pathway / : / : / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / extrinsic component of synaptic vesicle 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 / negative regulation of ubiquitin-dependent protein catabolic process / ERAD pathway / viral process / molecular adaptor activity / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Dutta, S. / Tan, Y.J. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural and Functional Characterization of Human Sgt and its Interaction with Vpu of the Human Immunodeficiency Virus Type 1. Authors: Dutta, S. / Tan, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vyi.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vyi.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 2vyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vyi_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 2vyi_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 2vyi_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 2vyi_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vyi ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vyi | HTTPS FTP |
-Related structure data
Related structure data | 1waoS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 14430.173 Da / Num. of mol.: 2 / Fragment: TETRATRICOPEPTIDE REPEAT, RESIDUES 84-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6FIA9, UniProt: O43765*PLUS #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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE |
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Crystal grow | Details: 4M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.95 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 12726 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.8 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WAO Resolution: 2.4→29.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1088998.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.7274 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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