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Open data
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Basic information
Entry | Database: PDB / ID: 4kgg | |||||||||
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Title | Crystal structure of light mutant2 and dcr3 complex | |||||||||
![]() | (Tumor necrosis factor ...) x 2 | |||||||||
![]() | Cytokine/Signaling Protein / LIGHT / DCR3 / TNF / TNFR / TNF14 / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW HVEM / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / CYTOKINE / IFN / JELLY-ROLL FOLD / BIND TNF RECEPTOR HVEM AND LTBR / LTBR / PROTEIN STRUCTURE INITIATIVE / ATOMS-TO-ANIMALS: THE IMMUNE FUNCTION NETWORK / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / IMMUNE SYSTEM / Cytokine-Signaling Protein complex | |||||||||
Function / homology | ![]() TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation ...TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation / T cell costimulation / T cell activation / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / signaling receptor activity / immune response / signaling receptor binding / apoptotic process / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, W. / Bonanno, J.B. / Zhan, C. / Kumar, P.R. / Toro, R. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC) | |||||||||
![]() | ![]() Title: Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly. Authors: Liu, W. / Zhan, C. / Cheng, H. / Kumar, P.R. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4en0C ![]() 4j6gSC ![]() 4kg8C ![]() 4kgqC C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Tumor necrosis factor ... , 2 types, 4 molecules CDAB
#1: Protein | Mass: 19044.217 Da / Num. of mol.: 2 / Fragment: 30-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 17208.436 Da / Num. of mol.: 2 / Fragment: 83-240 / Mutation: R195S, V196N, W198F, K214E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 47 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.49 % |
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Crystal grow | Temperature: 290 K / pH: 7 Details: 0.2 M Magnesium Chloride, 0.1 M Tris:HCl, 2.5 M Sodium Chloride, PH7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→50 Å / Num. obs: 27912 / % possible obs: 99.9 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.14 / Rsym value: 0.11 / Net I/σ(I): 20.1429 |
Reflection shell | Resolution: 2.78→2.83 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 4.12 / Rsym value: 0.648 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4J6G Resolution: 2.78→49.63 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.099 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.051 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→49.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.781→2.853 Å / Total num. of bins used: 20
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