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- PDB-1ext: EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ext | ||||||
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Title | EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21. | ||||||
![]() | TUMOR NECROSIS FACTOR RECEPTOR | ||||||
![]() | SIGNALLING PROTEIN / BINDING PROTEIN / CYTOKINE | ||||||
Function / homology | ![]() positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / TNFs bind their physiological receptors ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / tumor necrosis factor binding / TNF signaling / regulation of establishment of endothelial barrier / TNFR1-mediated ceramide production / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / prostaglandin metabolic process / positive regulation of execution phase of apoptosis / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naismith, J.H. / Sprang, S.R. | ||||||
![]() | ![]() Title: Structures of the extracellular domain of the type I tumor necrosis factor receptor. Authors: Naismith, J.H. / Devine, T.Q. / Kohno, T. / Sprang, S.R. #1: ![]() Title: Crystallographic Evidence for Dimerization of Unliganded Tumor Necrosis Factor Receptor Authors: Naismith, J.H. / Devine, T.Q. / Brandhuber, B.J. / Sprang, S.R. #2: ![]() Title: Two Crystal Forms of the Extracellular Domain of Type I Tumor Necrosis Factor Receptor Authors: Rodseth, L.E. / Brandhuber, B. / Devine, T.Q. / Eck, M.J. / Hale, K. / Naismith, J.H. / Sprang, S.R. #3: ![]() Title: Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnf Beta Complex: Implications for Tnf Receptor Activation Authors: Banner, D.W. / D'Arcy, A. / Janes, W. / Gentz, R. / Schoenfeld, H.J. / Broger, C. / Loetscher, H. / Lesslauer, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 446.1 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ncfS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18335.830 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: THE CONSTRUCT CONTAINS RESIDUES 12 TO 172 OF THE MATURE SEQUENCE OF THE ENTIRE RECEPTOR. RESIDUE 11 IS MUTATED TO MET AS A RESULT OF THE EXPRESSION SYSTEM Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.7 / Details: CRYSTALLIZED AT PH3.7 IN P 21 21 21. | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Rodseth, L.E., (1994) J.Mol.Biol., 239, 332. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Num. obs: 36977 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.85→1.93 Å / % possible all: 77 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 11 Å / Num. obs: 37300 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NCF Resolution: 1.85→8 Å / Cross valid method: FREE R / σ(F): 0 Details: ATOMS WITH ZERO OCCUPANCY ARE STEREOCHEMICALLY MODELED (68 OUT OF 2162) AND WERE NOT LOCATED IN EXPERIMENTAL MAPS.
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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