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Open data
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Basic information
Entry | Database: PDB / ID: 6pe8 | ||||||
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Title | Crystal structure of CD40/ABBV-323 FAB complex | ||||||
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![]() | IMMUNE SYSTEM / CD40 / FAB / complex | ||||||
Function / homology | ![]() cellular response to erythropoietin / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / response to peptide / positive regulation of protein kinase C signaling / varicosity / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex ...cellular response to erythropoietin / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / response to peptide / positive regulation of protein kinase C signaling / varicosity / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex / positive regulation of endothelial cell apoptotic process / B cell activation / response to cobalamin / B cell proliferation / defense response to protozoan / response to type II interferon / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of GTPase activity / antigen binding / TNFR2 non-canonical NF-kB pathway / positive regulation of MAP kinase activity / platelet activation / intracellular calcium ion homeostasis / cellular response to mechanical stimulus / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular response to tumor necrosis factor / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / inflammatory response / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / intracellular membrane-bounded organelle / neuronal cell body / ubiquitin protein ligase binding / enzyme binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Argiriadi, M.A. | ||||||
![]() | ![]() Title: CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches. Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / ...Authors: Argiriadi, M.A. / Benatuil, L. / Dubrovska, I. / Egan, D.A. / Gao, L. / Greischar, A. / Hardman, J. / Harlan, J. / Iyer, R.B. / Judge, R.A. / Lake, M. / Perron, D.C. / Sadhukhan, R. / Sielaff, B. / Sousa, S. / Wang, R. / McRae, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238 KB | Display | ![]() |
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PDB format | ![]() | 189.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pe7SC ![]() 6pe9C S: Starting model for refinement C: citing same article ( |
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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
#1: Antibody | Mass: 23748.588 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 24290.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 19187.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion / Details: 2M ammonium sulfate, 0.1M phosphate-citrate pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→173.2 Å / Num. obs: 40335 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.84→2.85 Å / Num. unique obs: 380 / CC1/2: 0.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6PE7 Resolution: 2.84→37.98 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 27.69 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→37.98 Å
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Refine LS restraints |
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LS refinement shell |
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