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- PDB-8pbv: Solution NMR structure of D. melanogaster TotA -

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Basic information

Entry
Database: PDB / ID: 8pbv
TitleSolution NMR structure of D. melanogaster TotA
ComponentsProtein Turandot A
KeywordsUNKNOWN FUNCTION / Turandot / antimicrobial peptide / TotA / stress
Function / homology
Function and homology information


response to mercury ion / response to water deprivation / response to methylmercury / response to UV / response to mechanical stimulus / response to cold / response to bacterium / cellular response to mechanical stimulus / cellular response to UV / cellular response to heat ...response to mercury ion / response to water deprivation / response to methylmercury / response to UV / response to mechanical stimulus / response to cold / response to bacterium / cellular response to mechanical stimulus / cellular response to UV / cellular response to heat / cellular response to oxidative stress / response to heat / response to oxidative stress / defense response to bacterium / innate immune response / extracellular space
Similarity search - Function
Stress-inducible humoral factor Turandot / Stress-inducible humoral factor Turandot
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / distance geometry
AuthorsAbriata, L.A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_215073 Switzerland
Swiss National Science FoundationCRSII5_186397 Switzerland
CitationJournal: Curr.Biol. / Year: 2024
Title: A humoral stress response protects Drosophila tissues from antimicrobial peptides.
Authors: Rommelaere, S. / Carboni, A. / Bada Juarez, J.F. / Boquete, J.P. / Abriata, L.A. / Teixeira Pinto Meireles, F. / Rukes, V. / Vincent, C. / Kondo, S. / Dionne, M.S. / Dal Peraro, M. / Cao, C. / Lemaitre, B.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Turandot A


Theoretical massNumber of molelcules
Total (without water)12,9901
Polymers12,9901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, NMR relaxation (as well as MALS and native MS) are all consistent with monomeric species in solution.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7820 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein Turandot A


Mass: 12989.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TotA, CG31509 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IN44

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-1H NOESY
133isotropic12D 1H-1H TOCSY
141isotropic13D 1H-15N TOCSY
151isotropic13D 1H-15N NOESY
162isotropic13D HNCA
172isotropic13D HN(CO)CA
182isotropic13D HNCO
1112isotropic13D HN(CA)CB
1102isotropic13D CBCA(CO)NH
191isotropic13D HNHA
1142isotropic13D (H)CCH-TOCSY
1132isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-15N] D. melanogaster TotA, 20 mM Mes pH 6, 100 mM sodium chloride, 90% H2O/10% D2OTotA_15N90% H2O/10% D2O
solution20.9 mM [U-13C; U-15N] D. melanogaster TotA, 20 mM Mes pH 6, 100 mM sodium chloride, 90% H2O/10% D2OTotA_13C_15N90% H2O/10% D2O
solution30.9 mM D. melanogaster TotA, 20 mM Mes pH 6, 100 mM sodium chloride, 90% H2O/10% D2OTotA_unlabeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMD. melanogaster TotA[U-15N]1
20 mMMes pH 6natural abundance1
100 mMsodium chloridenatural abundance1
0.9 mMD. melanogaster TotA[U-13C; U-15N]2
20 mMMes pH 6natural abundance2
100 mMsodium chloridenatural abundance2
0.9 mMD. melanogaster TotAnatural abundance3
20 mMMes pH 6natural abundance3
100 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 100 mM / Label: only condition / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARACARA NMR ETHchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
UNIOT. Hermannpeak picking
RefinementMethod: distance geometry / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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