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- PDB-4p4k: Structural Basis of Chronic Beryllium Disease: Bridging the Gap B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4p4k | ||||||
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Title | Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic hypersensitivity and auto immunity | ||||||
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![]() | IMMUNE SYSTEM / Be bound complex / Chronic beryllium disease / TCR-MHC peptide-Be2+ | ||||||
Function / homology | ![]() MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / immunoglobulin complex, circulating ...MHC class II receptor activity / alpha-beta T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / positive regulation of T cell proliferation / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / antigen binding / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / cell surface / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Clayton, G.M. / Crawford, F. / Kappler, J.W. | ||||||
![]() | ![]() Title: Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity. Authors: Clayton, G.M. / Wang, Y. / Crawford, F. / Novikov, A. / Wimberly, B.T. / Kieft, J.S. / Falta, M.T. / Bowerman, N.A. / Marrack, P. / Fontenot, A.P. / Dai, S. / Kappler, J.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345 KB | Display | ![]() |
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PDB format | ![]() | 272.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 522.7 KB | Display | ![]() |
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Full document | ![]() | 545.6 KB | Display | |
Data in XML | ![]() | 60.7 KB | Display | |
Data in CIF | ![]() | 84.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4p4rC ![]() 4p57C ![]() 4p5kC ![]() 4p5mC ![]() 3lqzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 21169.566 Da / Num. of mol.: 2 / Fragment: UNP residues 32-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 24394.152 Da / Num. of mol.: 2 / Fragment: UNP residues 32-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 22995.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 27266.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 1 types, 5 molecules ![](data/chem/img/NAG.gif)
#5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 334 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/0BE.gif)
![](data/chem/img/HOH.gif)
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#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8K, Na Cacodylate, glycerol / PH range: 5.5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 58169 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 78.7 Å2 / Net I/σ(I): 15.67 |
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Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3LQZ Resolution: 2.8→39.7 Å / Cor.coef. Fo:Fc: 0.9299 / Cor.coef. Fo:Fc free: 0.8869 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.959 / SU Rfree Blow DPI: 0.332 / SU Rfree Cruickshank DPI: 0.336
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Displacement parameters | Biso mean: 59.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.364 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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