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- PDB-2k1v: R3/I5 relaxin chimera -

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Basic information

Entry
Database: PDB / ID: 2k1v
TitleR3/I5 relaxin chimera
Components
  • Insulin-like peptide INSL5
  • Relaxin-3
KeywordsHORMONE / peptide hormone / relaxin-3 / insl5 / chimera / Cleavage on pair of basic residues / Secreted / SIGNALING PROTEIN
Function / homology
Function and homology information


Relaxin receptors / positive regulation of feeding behavior / G protein-coupled receptor binding / hormone activity / G alpha (i) signalling events / G alpha (s) signalling events / extracellular region
Similarity search - Function
Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Relaxin-3 / Insulin-like peptide INSL5
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
Model detailsSolution structure of the relaxin-3 B-chain / INSL5 A-chain chimeric peptide.
AuthorsRosengren, K. / Haugaard-Jonsson, L.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the R3/I5 Chimeric Relaxin Peptide, a Selective GPCR135 and GPCR142 Agonist.
Authors: Haugaard-Jonsson, L.M. / Hossain, M.A. / Daly, N.L. / Bathgate, R.A. / Wade, J.D. / Craik, D.J. / Rosengren, K.J.
History
DepositionMar 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Relaxin-3
A: Insulin-like peptide INSL5


Theoretical massNumber of molelcules
Total (without water)5,2502
Polymers5,2502
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Relaxin-3 / Prorelaxin H3 / Insulin-like peptide INSL7 / Insulin-like peptide 7


Mass: 3047.586 Da / Num. of mol.: 1 / Fragment: Relaxin-3 B chain / Source method: obtained synthetically
Details: Peptide chain was assembled by solid phase peptide synthesis.
References: UniProt: Q8WXF3
#2: Protein/peptide Insulin-like peptide INSL5 / Insulin-like peptide 5


Mass: 2202.509 Da / Num. of mol.: 1 / Fragment: Insulin-like peptide INSL5 A chain / Source method: obtained synthetically
Details: Peptide chain was assembled by solid phase peptide synthesis.
References: UniProt: Q9Y5Q6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the relaxin-3 B-chain / INSL5 A-chain chimeric peptide.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM relaxin-3 B-chain, 1 mM INSL5 A-chain, 90% H2O/10% D2O90% H2O/10% D2O
21 mM relaxin-3 B-chain, 1 mM INSL5 A-chain, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMrelaxin-3 B-chain1
1 mMINSL5 A-chain1
1 mMrelaxin-3 B-chain2
1 mMINSL5 A-chain2
Sample conditionsIonic strength: 0 / pH: 4 / 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
NameVersionDeveloperClassification
TopSpin1Bruker Biospincollection
TopSpin1Bruker Biospinprocessing
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures were generated using torsion angle dynamics in CNS and subsequently refined and energy minimized in a water shell using cartesian dynamics in CNS.
NMR constraintsNOE constraints total: 522 / NOE intraresidue total count: 0 / NOE long range total count: 243 / NOE medium range total count: 32 / NOE sequential total count: 247 / Hydrogen bond constraints total count: 20
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.29 Å

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