[English] 日本語
![](img/lk-miru.gif)
- PDB-5ys0: Crystal structure of the second StARkin domain of Lam2 in complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ys0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the second StARkin domain of Lam2 in complex with ergosterol | ||||||
![]() | Membrane-anchored lipid-binding protein YSP2 | ||||||
![]() | TRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / Ysp2 | ||||||
Function / homology | ![]() intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process ...intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / cortical endoplasmic reticulum / cholesterol transfer activity / cholesterol binding / cell periphery / mitochondrial membrane / apoptotic process / endoplasmic reticulum membrane / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tong, J. / Im, Y.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites Authors: Tong, J. / Manik, M.K. / Im, Y.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 82.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 813.9 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yqiC ![]() 5yqjC ![]() 5yqpC ![]() 5yqqC ![]() 5yqrC ![]() 4yqjS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19133.781 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: YSP2, LAM2, LTC4, YDR326C / Plasmid: pHIS2-Thr Details (production host): N-terminal hexahistidine tag fusion Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.86 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl pH 8.0, 30% PEG8000. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 16717 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 48.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 845 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4YQJ Resolution: 2.601→32.709 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.29
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→32.709 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|