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- PDB-2nav: NMR solution structure of Ex-4[1-16]/pl14a -

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Basic information

Entry
Database: PDB / ID: 2nav
TitleNMR solution structure of Ex-4[1-16]/pl14a
ComponentsExendin-4, Alpha/kappa-conotoxin pl14a chimera
KeywordsTOXIN / agonist
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / potassium channel regulator activity / hormone activity / regulation of blood pressure / toxin activity / extracellular region
Similarity search - Function
Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Exendin-4 / Alpha/kappa-conotoxin pl14a
Similarity search - Component
Biological speciesHeloderma suspectum (Gila monster)
Conus planorbis (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsSchroeder, C.I. / Swedberg, J.E. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Truncated Glucagon-like Peptide-1 and Exendin-4 alpha-Conotoxin pl14a Peptide Chimeras Maintain Potency and alpha-Helicity and Reveal Interactions Vital for cAMP Signaling in Vitro.
Authors: Swedberg, J.E. / Schroeder, C.I. / Mitchell, J.M. / Fairlie, D.P. / Edmonds, D.J. / Griffith, D.A. / Ruggeri, R.B. / Derksen, D.R. / Loria, P.M. / Price, D.A. / Liras, S. / Craik, D.J.
History
DepositionJan 11, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exendin-4, Alpha/kappa-conotoxin pl14a chimera


Theoretical massNumber of molelcules
Total (without water)3,1621
Polymers3,1621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Exendin-4, Alpha/kappa-conotoxin pl14a chimera


Mass: 3161.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Heloderma suspectum, Conus planorbis / References: UniProt: Q0N4U8, UniProt: P26349*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-1H COSY
1412D 1H-15N HSQC
1512D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.2 mM protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: H2O-1
Sample conditionspH: 3.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MolmolKoradi, Billeter and Wuthrichdata analysis
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
XEASYBrungerchemical shift assignment
XEASYBrungerpeak picking
XEASYBrungerchemical shift calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 333 / NOE intraresidue total count: 116 / NOE long range total count: 11 / NOE medium range total count: 72 / NOE sequential total count: 134
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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