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- PDB-1d0j: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M... -
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Basic information
Entry | Database: PDB / ID: 1d0j | ||||||
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Title | STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE | ||||||
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![]() | APOPTOSIS / B-SANDWICH / PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | ![]() CD40 receptor binding / tumor necrosis factor receptor superfamily complex / TNFs bind their physiological receptors / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / TNFs bind their physiological receptors / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / regulation of immature T cell proliferation in thymus / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / signal transduction involved in regulation of gene expression / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / mRNA stabilization / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / vesicle membrane / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein catabolic process / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / regulation of cell population proliferation / cell cortex / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / Ub-specific processing proteases / membrane raft / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / apoptotic process / protein kinase binding / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H. | ||||||
![]() | ![]() Title: The structural basis for the recognition of diverse receptor sequences by TRAF2. Authors: Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H. #1: ![]() Title: Structural basis for self-association and receptor recognition of human TRAF2 Authors: Park, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 202.9 KB | Display | ![]() |
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PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19006.916 Da / Num. of mol.: 6 / Fragment: TRAF DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 629.617 Da / Num. of mol.: 5 / Fragment: TRAF2-BINDING SEQUENCE / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN MOUSE (MUS MUSCULUS) References: UniProt: P20334 #3: Water | ChemComp-HOH / | Compound details | THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 6 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH ...THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 6 TRAF2 PER ASYMMETRIC | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / % possible obs: 90.2 % / Rmerge(I) obs: 0.061 |
Reflection shell | Highest resolution: 2.5 Å / Rmerge(I) obs: 0.296 / % possible all: 85.2 |
Reflection shell | *PLUS % possible obs: 85.2 % |
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Processing
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Refinement | Resolution: 2.5→20 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.227 / Rfactor obs: 0.227 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.27 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |