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Yorodumi- PDB-1tnr: CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN T... -
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-Basic information
Entry | Database: PDB / ID: 1tnr | ||||||
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Title | CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN TNF-BETA COMPLEX: IMPLICATIONS FOR TNF RECEPTOR ACTIVATION | ||||||
Components |
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Keywords | COMPLEX(LYMPHOKINE/RECEPTOR) / COMPLEX(LYMPHOKINE-RECEPTOR) / COMPLEX(LYMPHOKINE-RECEPTOR) complex | ||||||
Function / homology | Function and homology information positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of chronic inflammatory response to antigenic stimulus / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of chronic inflammatory response to antigenic stimulus / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / positive regulation of humoral immune response mediated by circulating immunoglobulin / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / humoral immune response / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / negative regulation of fibroblast proliferation / positive regulation of glial cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / response to nutrient / TNFR1-induced NF-kappa-B signaling pathway / cytokine activity / TNFR2 non-canonical NF-kB pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of type II interferon production / cell-cell signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / transcription by RNA polymerase II / response to hypoxia / receptor complex / defense response to Gram-positive bacterium / defense response to bacterium / response to xenobiotic stimulus / inflammatory response / positive regulation of apoptotic process / membrane raft / Golgi membrane / signaling receptor binding / apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.85 Å | ||||||
Authors | Banner, D.W. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1993 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. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and preliminary crystallographic analysis of a TNF-beta-55 kDa TNF receptor complex. Authors: D'Arcy, A. / Banner, D.W. / Janes, W. / Winkler, F.K. / Loetscher, H. / Schonfeld, H.J. / Zulauf, M. / Gentz, R. / Lesslauer, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tnr.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tnr.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/1tnr ftp://data.pdbj.org/pub/pdb/validation_reports/tn/1tnr | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15872.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01374 |
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#2: Protein | Mass: 15766.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: SF9 cells / References: UniProt: P19438 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.75 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.83 Å / Num. obs: 13270 / % possible obs: 99.7 % / Num. measured all: 43171 / Rmerge(I) obs: 0.078 |
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-Processing
Software |
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Refinement | Resolution: 2.85→50 Å / σ(F): 2 Details: THE RECEPTOR REGIONS R 15 - R 29 AND R 144 - R 153, I.E. THE N- AND C-TERMINAL ENDS OF THE RECEPTOR, MUST BE REGARDED AS TENTATIVE. THERE IS WEAK ELECTRON DENSITY FOR THE THREE CARBOHYDRATE ...Details: THE RECEPTOR REGIONS R 15 - R 29 AND R 144 - R 153, I.E. THE N- AND C-TERMINAL ENDS OF THE RECEPTOR, MUST BE REGARDED AS TENTATIVE. THERE IS WEAK ELECTRON DENSITY FOR THE THREE CARBOHYDRATE CHAINS ATTACHED TO ASPARAGINES R 25, R 116 AND R 122. THESE POSITIONS HAVE BEEN MARKED WITH WATER MOLECULES 45, 42 AND 43, RESPECTIVELY. ASPARTIC ACID A 50 ADOPTS THE UNUSUAL EPSILON CONFORMATION ON BINDING THE RECEPTOR. THE PEPTIDE PLANES A 40 - A 41 AND R 100 - R 101 MAY HAVE THE WRONG ORIENTATION.
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.8 |