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- PDB-6yxd: Room temperature structure of human adiponectin receptor 2 (ADIPO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yxd | ||||||||||||
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Title | Room temperature structure of human adiponectin receptor 2 (ADIPOR2) at 2.9 A resolution determined by Serial Crystallography (SSX) using CrystalDirect | ||||||||||||
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![]() | MEMBRANE PROTEIN / Adiponectin receptor / ADIPOR / serial synchrotron crystallography / SSX / 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 | ![]() | 225.5 KB | Display | ![]() |
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PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 27.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yx9C ![]() 6yxfC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#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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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 13160.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Antibody | Mass: 11647.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 63 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLB.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / | ||||||
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#5: Chemical | ChemComp-OLB / ( #6: Chemical | ChemComp-OLA / | #7: Chemical | ChemComp-GOL / | #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: 3.77 Å3/Da / Density % sol: 67.39 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: CrystalDirect-2 plates (MiTeGen) in 30 or 50 nL bolus overlaid with 600 nl precipitant solution. 42.3% PEG 400, 110 mM potassium citrate, 100 mM HEPES pH 7.0 for ADIPOR2. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 15292 / % possible obs: 100 % / Redundancy: 130.57 % / CC1/2: 0.98 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.9→2.98 Å / Num. unique obs: 1971 / CC1/2: 0.737 |
Serial crystallography sample delivery | Description: CrystalDirect-2 plate / Method: fixed target |
Serial crystallography data reduction | Crystal hits: 28949 / Frames indexed: 25297 / Frames total: 382552 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5LWY Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.825 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.419
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Displacement parameters | Biso mean: 48.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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