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- PDB-2l60: A novel design concept: New Y-receptor agonists with increased me... -

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Basic information

Entry
Database: PDB / ID: 2l60
TitleA novel design concept: New Y-receptor agonists with increased membrane recruitment, Y2 affinity and selectivity
ComponentsPeptide YY
KeywordsHORMONE / GPCR ligand
Function / homology
Function and homology information


neuropeptide Y receptor binding / intestinal epithelial cell differentiation / neuropeptide hormone activity / feeding behavior / neuropeptide signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #900 / Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPedersen, N.L. / Jurt, S. / Zerbe, O. / Jensen, K.J.
CitationJournal: To be Published
Title: A novel design concept: New Y-receptor agonists with increased membrane recruitment, Y2 affinity and selectivity
Authors: Pedersen, N.L. / Jurt, S. / Zerbe, O. / Jensen, K.J.
History
DepositionNov 11, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide YY


Theoretical massNumber of molelcules
Total (without water)5,1221
Polymers5,1221
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide YY / PYY / PYY-I / Peptide tyrosine tyrosine / Peptide YY(3-36) / PYY-II


Mass: 5121.941 Da / Num. of mol.: 1 / Fragment: UNP residues 41-64 / Source method: obtained synthetically / References: UniProt: P10082
Sequence detailsTHE DEPOSITED SEQUENCE IS A DESIGNED VARIANT OF THE PEPTIDE PYY. THE C-TERMINAL RESIDUES CORRESPOND ...THE DEPOSITED SEQUENCE IS A DESIGNED VARIANT OF THE PEPTIDE PYY. THE C-TERMINAL RESIDUES CORRESPOND TO THE SEQUENCE OF HUMAN PYY, THE N-TERMINAL SEGMENT WAS REPLACED WITH A DESIGNED SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of a (3-36)PYY mutant for improved membrane-binding affinity and improved Y2 receptor binding in presence of a membrane model (DPC)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM entity, 1 mM RNH, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMentity_1-11
1 mMRNH-21
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3P.GUNTERT ET AL.structure solution
Amber6Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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