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- PDB-7at7: Transmembrane helix of tumor necrosis factor alpha in trifluoreth... -

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Basic information

Entry
Database: PDB / ID: 7at7
TitleTransmembrane helix of tumor necrosis factor alpha in trifluorethanol, S34P mutant
ComponentsTumor necrosis factor
KeywordsMEMBRANE PROTEIN / Transmembrane domain / helix / Trifluorethanol
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 / negative regulation of amyloid-beta clearance / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / death receptor agonist activity / 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
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGuschtschin-Schmidt, N. / Muhle-Goll, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)MU1606/6-2 Germany
CitationJournal: Iscience / Year: 2020
Title: Non-canonical Shedding of TNF alpha by SPPL2a Is Determined by the Conformational Flexibility of Its Transmembrane Helix.
Authors: Spitz, C. / Schlosser, C. / Guschtschin-Schmidt, N. / Stelzer, W. / Menig, S. / Gotz, A. / Haug-Kroper, M. / Scharnagl, C. / Langosch, D. / Muhle-Goll, C. / Fluhrer, R.
History
DepositionOct 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)3,7121
Polymers3,7121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3660 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures 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: 3711.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01375

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 0.5 mM TNFa_TM_S34P, trifluoroethanol/water / Label: 1H_sample / Solvent system: trifluoroethanol/water
SampleConc.: 0.5 mM / Component: TNFa_TM_S34P / Isotopic labeling: natural abundance
Sample conditionsDetails: 80% TFE-d2/20% dH2O with 5 mM TCEP / Ionic strength: 0 M / Ionic strength err: 0.01 / Label: conditions_1 / pH: 6.0 / PH err: 0.3 / Pressure: 1 atm / Temperature: 303 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
CcpNmr Analysis2.4.1CCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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