[English] 日本語
![](img/lk-miru.gif)
- PDB-6oaz: Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6oaz | ||||||
---|---|---|---|---|---|---|---|
Title | Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in HEK293-F cells | ||||||
![]() |
| ||||||
![]() | HYDROLASE/PROTEIN BINDING / Lipase / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() chylomicron binding / positive regulation of chylomicron remnant clearance / lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / response to heparin / positive regulation of cholesterol storage / lipoprotein lipase activator activity ...chylomicron binding / positive regulation of chylomicron remnant clearance / lipoprotein lipase / lipoprotein lipase activity / positive regulation of sequestering of triglyceride / low-density lipoprotein particle mediated signaling / chylomicron remodeling / response to heparin / positive regulation of cholesterol storage / lipoprotein lipase activator activity / lipase binding / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / triglyceride catabolic process / phospholipase activity / Assembly of active LPL and LIPC lipase complexes / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of lipoprotein lipase activity / protein transporter activity / very-low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / Chylomicron remodeling / positive regulation of lipid storage / acetylcholine receptor inhibitor activity / cellular response to nutrient / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle / transcytosis / protein import / triacylglycerol lipase activity / heparan sulfate proteoglycan binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / protein localization to cell surface / triglyceride homeostasis / cellular response to fatty acid / triglyceride metabolic process / lipoprotein particle binding / apolipoprotein binding / catalytic complex / positive regulation of fat cell differentiation / phospholipid metabolic process / response to glucose / positive regulation of chemokine production / Retinoid metabolism and transport / protein-membrane adaptor activity / positive regulation of adipose tissue development / fatty acid metabolic process / positive regulation of interleukin-1 beta production / cholesterol homeostasis / response to bacterium / intracellular protein transport / fatty acid biosynthetic process / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / heparin binding / basolateral plasma membrane / protein stabilization / apical plasma membrane / external side of plasma membrane / signaling receptor binding / lipid binding / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arora, R. / Horton, P.A. / Benson, T.E. / Romanowski, M.J. | ||||||
![]() | ![]() Title: Structure of lipoprotein lipase in complex with GPIHBP1. Authors: Arora, R. / Nimonkar, A.V. / Baird, D. / Wang, C. / Chiu, C.H. / Horton, P.A. / Hanrahan, S. / Cubbon, R. / Weldon, S. / Tschantz, W.R. / Mueller, S. / Brunner, R. / Lehr, P. / Meier, P. / ...Authors: Arora, R. / Nimonkar, A.V. / Baird, D. / Wang, C. / Chiu, C.H. / Horton, P.A. / Hanrahan, S. / Cubbon, R. / Weldon, S. / Tschantz, W.R. / Mueller, S. / Brunner, R. / Lehr, P. / Meier, P. / Ottl, J. / Voznesensky, A. / Pandey, P. / Smith, T.M. / Stojanovic, A. / Flyer, A. / Benson, T.E. / Romanowski, M.J. / Trauger, J.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 805.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 679.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 291.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 291.9 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oauC ![]() 6ob0C ![]() 1lpaS ![]() 2j8bS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 50465.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 14727.757 Da / Num. of mol.: 4 / Fragment: residues 21-151 / Mutation: N78D, N82D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Sugars , 1 types, 8 molecules ![](data/chem/img/NAG.gif)
#3: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 3 types, 37 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15M calcium acetate, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.04→191.94 Å / Num. obs: 55090 / % possible obs: 97.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 85.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.049 / Rrim(I) all: 0.117 / Net I/σ(I): 10.6 / Num. measured all: 303821 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1LPA, 2J8B Resolution: 3.04→121.52 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.6 Å2 / Biso mean: 113.11 Å2 / Biso min: 16.12 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.04→121.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.04→3.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | T11: 0.6079 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|