+Open data
-Basic information
Entry | Database: PDB / ID: 1fll | ||||||
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Title | MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 | ||||||
Components |
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Keywords | APOPTOSIS / TRAF3 WITH CD40 PEPTIDE / TNF SIGNALING | ||||||
Function / homology | Function and homology information CD154 receptor binding / cellular response to erythropoietin / regulation of interferon-beta production / response to peptide / TRAF3 deficiency - HSE / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity ...CD154 receptor binding / cellular response to erythropoietin / regulation of interferon-beta production / response to peptide / TRAF3 deficiency - HSE / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / serine/threonine protein kinase complex / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / regulation of proteolysis / thioesterase binding / positive regulation of endothelial cell apoptotic process / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / B cell activation / response to cobalamin / B cell proliferation / response to type II interferon / defense response to protozoan / protein K63-linked ubiquitination / positive regulation of type I interferon production / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / ubiquitin ligase complex / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of cytokine production / tumor necrosis factor-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interleukin-12 production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / phosphatidylinositol 3-kinase/protein kinase B signal transduction / antigen binding / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / positive regulation of MAP kinase activity / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / platelet activation / positive regulation of GTPase activity / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / ubiquitin-protein transferase activity / positive regulation of angiogenesis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ubiquitin protein ligase activity / Ovarian tumor domain proteases / signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / TRAF3-dependent IRF activation pathway / regulation of apoptotic process / protein phosphatase binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cellular response to lipopolysaccharide / endosome membrane / endosome / inflammatory response / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / intracellular membrane-bounded organelle / neuronal cell body / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å | ||||||
Authors | Ni, C.-Z. / Welsh, K. / Leo, E. / Chiou, C.-K. / Wu, H. / Reed, J.C. / Ely, K.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Molecular basis for CD40 signaling mediated by TRAF3. Authors: Ni, C.Z. / Welsh, K. / Leo, E. / Chiou, C.K. / Wu, H. / Reed, J.C. / Ely, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fll.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fll.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1fll ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1fll | HTTPS FTP |
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-Related structure data
-Links
-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
#1: Protein | Mass: 25885.521 Da / Num. of mol.: 2 / Fragment: TRAF DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13114 #2: Protein/peptide | Mass: 2195.341 Da / Num. of mol.: 2 / Fragment: CD40 (246-266) PEPTIDE / Mutation: N246K, C258S / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS) References: UniProt: P25942 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.87 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 29115 / % possible obs: 78.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14 |
Reflection shell | Resolution: 3.5→3.63 Å / Rmerge(I) obs: 0.26 / % possible all: 74.5 |
Reflection shell | *PLUS % possible obs: 74.5 % |
-Processing
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Refinement | Resolution: 3.5→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
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Refine LS restraints |
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