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Yorodumi- PDB-1i9r: STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i9r | ||||||
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Title | STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED 5C8 ANTIBODY | ||||||
Components |
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Keywords | CYTOKINE/IMMUNE SYSTEM / beta-sheet sandwich / immunoglobulin / CYTOKINE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information CD40 receptor binding / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / isotype switching / positive regulation of endothelial cell apoptotic process / tumor necrosis factor receptor binding / regulation of immunoglobulin production / leukocyte cell-cell adhesion / B cell proliferation / positive regulation of interleukin-10 production ...CD40 receptor binding / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / isotype switching / positive regulation of endothelial cell apoptotic process / tumor necrosis factor receptor binding / regulation of immunoglobulin production / leukocyte cell-cell adhesion / B cell proliferation / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-12 production / protein serine/threonine kinase activator activity / B cell differentiation / cytokine activity / TNFR2 non-canonical NF-kB pathway / integrin-mediated signaling pathway / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / positive regulation of NF-kappaB transcription factor activity / inflammatory response / external side of plasma membrane / negative regulation of apoptotic process / Golgi apparatus / cell surface / extracellular space / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Karpusas, M. / Lucci, J. / Ferrant, J. / Benjamin, C. / Hsu, Y.-M. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of CD40 ligand in complex with the Fab fragment of a neutralizing humanized antibody. Authors: Karpusas, M. / Lucci, J. / Ferrant, J. / Benjamin, C. / Taylor, F.R. / Strauch, K. / Garber, E. / Hsu, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i9r.cif.gz | 329.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i9r.ent.gz | 267 KB | Display | PDB format |
PDBx/mmJSON format | 1i9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9r ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9r | HTTPS FTP |
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-Related structure data
Related structure data | 1alyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15812.817 Da / Num. of mol.: 3 / Fragment: RESIDUES 116-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P29965 #2: Antibody | Mass: 23304.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: NSO MYELOMA #3: Antibody | Mass: 23881.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: NSO MYELOMA #4: Chemical | |
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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: 3.1 Å3/Da / Density % sol: 60.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 11, 1999 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→35 Å / Num. all: 71662 / Num. obs: 46508 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.52 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 1.97 / % possible all: 87.7 |
Reflection | *PLUS Lowest resolution: 35 Å |
Reflection shell | *PLUS % possible obs: 87.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1aly Resolution: 3.1→35 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: For NCS the following 3 chain groups were used: a) A, H, L, b) B,K, X c) C, M, Y. The final rms deviation of main chain atoms between groups is 0.18 Angstrom.
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Refinement step | Cycle: LAST / Resolution: 3.1→35 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |