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- PDB-5yqq: Crystal structure of a domain-swapped dimer of the second StARkin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yqq | ||||||
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Title | Crystal structure of a domain-swapped dimer of the second StARkin domain of Lam2 | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.7 KB | Display | ![]() |
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PDB format | ![]() | 60 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yqiC ![]() 5yqjSC ![]() 5yqpC ![]() 5yqrC ![]() 5ys0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19133.781 Da / Num. of mol.: 2 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): An N-terminal hexa-histidine tag fusion Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 25976 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1273 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YQJ Resolution: 1.9→24.017 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24.017 Å
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Refine LS restraints |
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LS refinement shell |
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