+Open data
-Basic information
Entry | Database: PDB / ID: 5m2j | ||||||
---|---|---|---|---|---|---|---|
Title | Complex between human TNF alpha and Llama VHH2 | ||||||
Components |
| ||||||
Keywords | CYTOKINE / human TNF alpha Llama VHH2 | ||||||
Function / homology | Function and homology information 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 / : / response to macrophage colony-stimulating factor / positive regulation of vitamin D biosynthetic process / 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 / negative regulation of amyloid-beta clearance / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / 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 / positive regulation of action potential / sequestering of triglyceride / TNF signaling / positive regulation of protein transport / positive regulation of interleukin-18 production / 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 / leukocyte tethering or rolling / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / positive regulation of protein localization to cell surface / negative regulation of glucose import / TNFR1-mediated ceramide production / endothelial cell apoptotic process / regulation of establishment of endothelial barrier / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / negative regulation of oxidative phosphorylation / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of protein-containing complex disassembly / positive regulation of programmed cell death / positive regulation of hepatocyte proliferation / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / positive regulation of heterotypic cell-cell adhesion / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / 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 / cortical actin cytoskeleton organization / response to L-glutamate / positive regulation of DNA biosynthetic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / 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 / negative regulation of interleukin-6 production / phagocytic cup / antiviral innate immune response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / skeletal muscle contraction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cambillau, C. / Spinelli, S. / Desmyter, A. / de Haard, H. | ||||||
Citation | Journal: Front Immunol / Year: 2017 Title: Bivalent Llama Single-Domain Antibody Fragments against Tumor Necrosis Factor Have Picomolar Potencies due to Intramolecular Interactions. Authors: Beirnaert, E. / Desmyter, A. / Spinelli, S. / Lauwereys, M. / Aarden, L. / Dreier, T. / Loris, R. / Silence, K. / Pollet, C. / Cambillau, C. / de Haard, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5m2j.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m2j.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2j ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2j | HTTPS FTP |
---|
-Related structure data
Related structure data | 5m2iSC 5m2mC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17370.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01375 |
---|---|
#2: Antibody | Mass: 12618.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 to 300 nL of protein at 11 mg per ml in HEPES 10 mM pH 7.0 with 100 nL of precipitant solution containing 12% 130 mM NaCl and 366 mM CaCl2 and 70 mM CAPS pH 9.0 and 30 mM MES pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.3 Å / Num. obs: 21089 / % possible obs: 97.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 11 / CC1/2: 0.98 / % possible all: 94.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M2I Resolution: 1.9→48.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9211 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.124
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.78 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→48.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|