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- PDB-7vpr: Crystal structure of the ligand-binding domain of C. glabrata Upc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vpr | ||||||
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Title | Crystal structure of the ligand-binding domain of C. glabrata Upc2 in complex with ergosterol | ||||||
![]() | Sterol uptake control protein 2 (Upc2) | ||||||
![]() | TRANSCRIPTION / ergosterol / transcription factor / ligand-binding / zinc finger | ||||||
Function / homology | ![]() ergosterol biosynthetic process / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, L. / Im, Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for activation of fungal sterol receptor Upc2 and azole resistance. Authors: Tan, L. / Chen, L. / Yang, H. / Jin, B. / Kim, G. / Im, Y.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.2 KB | Display | ![]() |
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PDB format | ![]() | 188.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vpsC ![]() 7vptC ![]() 7vpuC ![]() 7xb5C ![]() 4n9nS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 34242.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): N-terminal thrombin-cleavable hexa-histidine tag Production host: ![]() ![]() #2: Chemical | ChemComp-ERG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M Na-Acetate pH 4.0, 10% PEG 4000, 0.1 M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 34631 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 44.46 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.391 / Num. unique obs: 1404 / % possible all: 79.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4N9N Resolution: 2.59→27.6 Å / SU ML: 0.3441 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0387 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: 51.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→27.6 Å
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Refine LS restraints |
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LS refinement shell |
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