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- PDB-7qlf: Conformational ensemble of solnatide in solution -

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Basic information

Entry
Database: PDB / ID: 7qlf
TitleConformational ensemble of solnatide in solution
ComponentsTumor necrosis factor
KeywordsDE NOVO PROTEIN / synthetic peptide / solnatide
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 fractalkine production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of protein transport ...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 fractalkine production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of protein transport / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / response to 3,3',5-triiodo-L-thyronine / positive regulation of translational initiation by iron / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / response to macrophage colony-stimulating factor / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / response to gold nanoparticle / negative regulation of myelination / negative regulation of vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of interleukin-18 production / inflammatory response to wounding / death receptor agonist activity / positive regulation of action potential / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / negative regulation of D-glucose import / embryonic digestive tract development / leukocyte migration involved in inflammatory response / vascular endothelial growth factor production / positive regulation of fever generation / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / necroptotic signaling pathway / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / regulation of establishment of endothelial barrier / positive regulation of protein-containing complex disassembly / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / cellular response to toxic substance / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / negative regulation of systemic arterial blood pressure / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of programmed cell death / negative regulation of mitotic cell cycle / positive regulation of membrane protein ectodomain proteolysis / positive regulation of podosome assembly / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of canonical NF-kappaB signal transduction / response to L-glutamate / regulation of fat cell differentiation / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / negative regulation of bicellular tight junction assembly / regulation of reactive oxygen species metabolic process / regulation of metabolic process / positive regulation of DNA biosynthetic process / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of amyloid-beta formation / response to isolation stress / regulation of synapse organization / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / positive regulation of JUN kinase activity / positive regulation of MAP kinase activity / Interleukin-10 signaling / negative regulation of interleukin-6 production / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / cell surface receptor signaling pathway via JAK-STAT / negative regulation of osteoblast differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / skeletal muscle contraction / detection of mechanical stimulus involved in sensory perception of pain
Similarity search - Function
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsMODEL GENERATED BY ROSETTA VERSION 2020.08+release.cb1cabafd74
AuthorsMacias, M.J. / Martin-Malpartida, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Conformational ensemble of the TNF-derived peptide solnatide in solution.
Authors: Martin-Malpartida, P. / Arrastia-Casado, S. / Farrera-Sinfreu, J. / Lucas, R. / Fischer, H. / Fischer, B. / Eaton, D.C. / Tzotzos, S. / Macias, M.J.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)1,9271
Polymers1,9271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 1927.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SOlnatide, a peptide derived from hTNF with ENac activating effect.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01375
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TOCSY
121isotropic12D NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM solnatide, 90% H2O/10% D2O / Label: 1H_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: solnatide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: condition1 / pH: 5 / Pressure: 1 atm / Temperature: 290 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 30

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