[English] 日本語
![](img/lk-miru.gif)
- PDB-1tnf: THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 ANGSTROMS RES... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1tnf | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 ANGSTROMS RESOLUTION. IMPLICATIONS FOR RECEPTOR BINDING | ||||||
![]() | TUMOR NECROSIS FACTOR-ALPHA | ||||||
![]() | LYMPHOKINE | ||||||
Function / homology | ![]() negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : / positive regulation of vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / response to isolation stress / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / sequestering of triglyceride / positive regulation of interleukin-18 production / positive regulation of action potential / TNF signaling / positive regulation of protein transport / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / negative regulation of oxidative phosphorylation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / regulation of synapse organization / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of interleukin-6 production / phagocytic cup / antiviral innate immune response / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / skeletal muscle contraction Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Eck, M.J. / Sprang, S.R. | ||||||
![]() | ![]() Title: The structure of tumor necrosis factor-alpha at 2.6 A resolution. Implications for receptor binding. Authors: Eck, M.J. / Sprang, S.R. #1: ![]() Title: Crystallization of Trimeric Recombinant Human Tumor Necrosis Factor (Cachectin) Authors: Eck, M.J. / Beutler, B. / Kuo, G. / Merryweather, J.P. / Sprang, S.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 414 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Atom site foot note | 1: SEE REMARK 4. / 2: SEE REMARK 5. | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | THE MOLECULE EXISTS AS A TRIMER IN WHICH THE THREE SUBUNITS ARE RELATED BY APPROXIMATE THREE-FOLD SYMMETRY. THE THREE SUBUNITS HAVE BEEN ASSIGNED CHAIN INDICATORS A, B, AND C. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN B. |
-
Components
#1: Protein | Mass: 17368.729 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
---|---|
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 5.5 / Method: unknown |
Components of the solutions | *PLUS Conc.: 2.6 M / Common name: magnesium sulfate |
-Data collection
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 17097 / % possible obs: 72.1 % / Observed criterion σ(I): 2 / Num. measured all: 126662 / Rmerge(I) obs: 0.065 |
---|
-
Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.23 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|