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- PDB-5dmi: Structure of the extracellular domain of the CD40 in complex with... -
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Basic information
Entry | Database: PDB / ID: 5dmi | ||||||
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Title | Structure of the extracellular domain of the CD40 in complex with CHI220 FAB | ||||||
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![]() | IMMUNE SYSTEM/SIGNALING PROTEIN / CELL SURFACE RECEPTOR / ANTIBODY-ANTIGEN COMPLEX / ANTITUMOR / IMMUNE SYSTEM-SIGNALING PROTEIN complex | ||||||
Function / homology | ![]() CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes ...CD154 receptor binding / cellular response to erythropoietin / response to peptide / B cell mediated immunity / immune response-regulating cell surface receptor signaling pathway / positive regulation of protein kinase C signaling / CD40 signaling pathway / varicosity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of isotype switching to IgG isotypes / CD40 receptor complex / TRIF-dependent toll-like receptor signaling pathway / 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 / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-1 / 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 / TNFR2 non-canonical NF-kB pathway / antigen binding / 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 | ![]() ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() Title: Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope. Authors: Yamniuk, A.P. / Suri, A. / Krystek, S.R. / Tamura, J. / Ramamurthy, V. / Kuhn, R. / Carroll, K. / Fleener, C. / Ryseck, R. / Cheng, L. / An, Y. / Drew, P. / Grant, S. / Suchard, S.J. / ...Authors: Yamniuk, A.P. / Suri, A. / Krystek, S.R. / Tamura, J. / Ramamurthy, V. / Kuhn, R. / Carroll, K. / Fleener, C. / Ryseck, R. / Cheng, L. / An, Y. / Drew, P. / Grant, S. / Suchard, S.J. / Nadler, S.G. / Bryson, J.W. / Sheriff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.8 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.5 KB | Display | ![]() |
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Full document | ![]() | 466.6 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dmjC ![]() 5ihlC ![]() 1jmaS ![]() 1ncfS ![]() 1tnrS ![]() 2aw2S ![]() 2hevS ![]() 2heyS ![]() 2o5xS ![]() 2uwiS ![]() 2zpkS ![]() 3d85S 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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Unit cell |
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Components
#1: Protein | Mass: 20084.449 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 23-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Antibody | Mass: 23908.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: ![]() ![]() | ||||
#3: Antibody | Mass: 23361.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: ![]() ![]() | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE AUTHOR STATES THAT THE PROTEIN WAS EXPRESSED WITH ASN153 AND ASN180 (AND POST-TRANSLATIONAL ...THE AUTHOR STATES THAT THE PROTEIN WAS EXPRESSED WITH ASN153 AND ASN180 (AND POST-TRANSLATIO | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 80mM sodiym acetate, pH 4.6, 1.6 M ammonium sulfate, 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.69→201.15 Å / Num. obs: 14668 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 11.33 Å2 / Rsym value: 0.249 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3.69→3.89 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 6.8 / Rejects: 0 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X Resolution: 3.69→32.64 Å / Cor.coef. Fo:Fc: 0.9002 / Cor.coef. Fo:Fc free: 0.8676 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.397
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Displacement parameters | Biso max: 121.46 Å2 / Biso mean: 42.89 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.69→32.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.69→3.98 Å / Total num. of bins used: 7
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