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- PDB-8glg: Crystal Structure of Human CD1b in Complex with Phosphatidylethan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8glg | ||||||
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Title | Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1 | ||||||
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Function / homology | ![]() endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shahine, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms. Authors: Huang, S. / Shahine, A. / Cheng, T.Y. / Chen, Y.L. / Ng, S.W. / Balaji, G.R. / Farquhar, R. / Gras, S. / Hardman, C.S. / Altman, J.D. / Tahiri, N. / Minnaard, A.J. / Ogg, G.S. / Mayfield, J. ...Authors: Huang, S. / Shahine, A. / Cheng, T.Y. / Chen, Y.L. / Ng, S.W. / Balaji, G.R. / Farquhar, R. / Gras, S. / Hardman, C.S. / Altman, J.D. / Tahiri, N. / Minnaard, A.J. / Ogg, G.S. / Mayfield, J.A. / Rossjohn, J. / Moody, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.9 KB | Display | ![]() |
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PDB format | ![]() | 146 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gleC ![]() 8glfC ![]() 8glhC ![]() 8gliC ![]() 5l2kS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 , 2 types, 2 molecules AB
#1: Protein | Mass: 33530.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11974.456 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide ![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 7 types, 554 molecules ![](data/chem/img/L9Q.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/CUY.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/CUY.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-L9Q / ( | ||||||
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#6: Chemical | ChemComp-NI / ![]() | ||||||
#7: Chemical | ChemComp-CUY / | ||||||
#8: Chemical | ChemComp-CL / ![]() #9: Chemical | ![]() #10: Chemical | ChemComp-EDO / ![]() #11: 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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 27% PEG3350, 0.1 M sodium iodide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→46.49 Å / Num. obs: 57434 / % possible obs: 98.8 % / Redundancy: 14.9 % / CC1/2: 0.99 / Rpim(I) all: 0.041 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2741 / CC1/2: 0.73 / Rpim(I) all: 0.541 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5L2K Resolution: 1.6→36.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.099 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.087
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Displacement parameters | Biso mean: 25.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→36.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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