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- PDB-6yxf: Cryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 liga... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yxf | ||||||||||||
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Title | Cryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 ligand determined by Serial Crystallography (SSX) using CrystalDirect | ||||||||||||
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![]() | MEMBRANE PROTEIN / Adiponectin receptor / ADIPOR2 / serial synchrotron crystallography / SSX / ligand soaking / CrystalDirect / LCP crystallization / in meso / membrane proteins | ||||||||||||
Function / homology | ![]() adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis ...adiponectin binding / adipokinetic hormone receptor activity / adiponectin-activated signaling pathway / AMPK inhibits chREBP transcriptional activation activity / vascular wound healing / fatty acid oxidation / hormone-mediated signaling pathway / glucose homeostasis / signaling receptor activity / positive regulation of cold-induced thermogenesis / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: An automated platform for structural analysis of membrane proteins through serial crystallography. Authors: Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Cong, X. / Golebiowski, J. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 97 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yx9C ![]() 6yxdC ![]() 6yxgC ![]() 6yxhC ![]() 5lwyS 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
-Protein / Antibody , 2 types, 2 molecules AH
#1: Protein | Mass: 33097.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 24904.604 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 58 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/GD.gif)
![](data/chem/img/DO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/GD.gif)
![](data/chem/img/DO3.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | ChemComp-OLA / | ||||||
#5: Chemical | ChemComp-OLB / ( #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.84 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, ...Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution using either a Mosquito LCP robot (SPT Labtech) in CrystalDirect plate-2. The crystallisation condition is made of 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0. 60-120 nL of Gd-DO3 soaking solution with a final conc. of 10 - 25 mM was delivered onto LCP crystallisation drop. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.72 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 31468 / % possible obs: 100 % / Redundancy: 14.98 % / CC1/2: 0.98 / Net I/σ(I): 5.06 |
Reflection shell | Resolution: 3.01→3.1 Å / Num. unique obs: 2336 / CC1/2: 0.3 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LWY Resolution: 3.025→48.67 Å / Cor.coef. Fo:Fc: 0.826 / Cor.coef. Fo:Fc free: 0.82 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.394
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Displacement parameters | Biso max: 300 Å2 / Biso mean: 81.24 Å2 / Biso min: 36.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.025→48.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.025→3.06 Å / Rfactor Rfree error: 0
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