+Open data
-Basic information
Entry | Database: PDB / ID: 5m2m | ||||||
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Title | Complex between human TNF alpha and Llama VHH3 | ||||||
Components |
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Keywords | CYTOKINE / human TNF alpha / Llama nanobody | ||||||
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 / positive regulation of vitamin D biosynthetic process ...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 / : / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / 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 / response to isolation stress / 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 / 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 / positive regulation of mononuclear cell migration / leukocyte tethering or rolling / response to fructose / positive regulation of synoviocyte proliferation / positive regulation of fever generation / negative regulation of myoblast differentiation / regulation of establishment of endothelial barrier / negative regulation of glucose import / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / negative regulation of oxidative phosphorylation / TNFR1-mediated ceramide production / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / regulation of metabolic process / 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 protein-containing complex disassembly / positive regulation of heterotypic cell-cell adhesion / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / regulation of canonical NF-kappaB signal transduction / negative regulation of mitotic cell cycle / regulation of reactive oxygen species metabolic process / regulation of fat cell differentiation / TNFR1-induced proapoptotic signaling / positive regulation of leukocyte adhesion to vascular endothelial cell / cortical actin cytoskeleton organization / response to L-glutamate / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / negative regulation of osteoblast differentiation / regulation of synapse organization / negative regulation of fat cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / regulation of insulin secretion / positive regulation of glial cell proliferation / phagocytic cup / humoral immune response / negative regulation of signaling receptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m2m.cif.gz | 651.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m2m.ent.gz | 541 KB | Display | PDB format |
PDBx/mmJSON format | 5m2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m2m_validation.pdf.gz | 522.6 KB | Display | wwPDB validaton report |
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Full document | 5m2m_full_validation.pdf.gz | 561.1 KB | Display | |
Data in XML | 5m2m_validation.xml.gz | 65.8 KB | Display | |
Data in CIF | 5m2m_validation.cif.gz | 90.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2m ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2m | HTTPS FTP |
-Related structure data
Related structure data | 5m2iSC 5m2jC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17370.658 Da / Num. of mol.: 6 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: 14196.523 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria) #3: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: mixing 100 to 300 nL of protein (9 mg per ml in HEPES 10 mM pH 7.0) with 100 nL of precipitant solution containing: 9% PEG3350, 8% PEG-MME550, 130 mM NaSO4, 70 mM BTP, 30 mM Mes, and 3 mM ZnSO4, 8.5 PH range: 7 - 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 62613 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.04 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.1 / CC1/2: 0.96 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M2I Resolution: 2.3→29.59 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.9178 / SU R Cruickshank DPI: 0.61 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.622 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.264
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Displacement parameters | Biso mean: 45.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.396 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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