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- PDB-2h8b: Solution structure of INSL3 -

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Basic information

Entry
Database: PDB / ID: 2h8b
TitleSolution structure of INSL3
Components(Insulin-like 3) x 2
KeywordsHORMONE/GROWTH FACTOR / INSULIN/RELAXIN SUPARFAMILY FOLD / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Relaxin receptors / oocyte maturation / positive regulation of wound healing / positive regulation of cAMP/PKA signal transduction / positive regulation of epithelial cell migration / insulin receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / hormone activity / cell-cell signaling / protease binding ...Relaxin receptors / oocyte maturation / positive regulation of wound healing / positive regulation of cAMP/PKA signal transduction / positive regulation of epithelial cell migration / insulin receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / hormone activity / cell-cell signaling / protease binding / G alpha (s) signalling events / spermatogenesis / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / extracellular space / extracellular region
Similarity search - Function
Insulin-like INSL3/INSL4 / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics, cartesian dynamics
AuthorsRosengren, K.J. / Craik, D.J. / Daly, N.L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Solution Structure and Characterization of the LGR8 Receptor Binding Surface of Insulin-like Peptide 3
Authors: Rosengren, K.J. / Zhang, S. / Lin, F. / Daly, N.L. / Scott, D.J. / Hughes, R.A. / Bathgate, R.A.D. / Craik, D.J. / Wade, J.D.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Insulin-like 3
A: Insulin-like 3


Theoretical massNumber of molelcules
Total (without water)6,3062
Polymers6,3062
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 least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Insulin-like 3 / Insulin-Like Peptide-3 / INSL3 / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor


Mass: 3528.118 Da / Num. of mol.: 1 / Fragment: Insulin-like 3 B chain / Source method: obtained synthetically
Details: For this study the peptide has been generated by solid phase peptide synthesis.; This sequence occurs naturally in humans.
References: UniProt: P51460
#2: Protein/peptide Insulin-like 3 / Insulin-Like Peptide-3 / INSL3 / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor


Mass: 2778.189 Da / Num. of mol.: 1 / Fragment: Insulin-like 3 A chain / Source method: obtained synthetically
Details: For this study the peptide has been generated by solid phase peptide synthesis.; This sequence occurs naturally in humans.
References: UniProt: P51460
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY
2712D TOCSY
2812D NOESY
2922D NOESY
21022D TOCSY
31112D TOCSY
31212D NOESY
31322D NOESY
31422D TOCSY
41512D TOCSY
41612D NOESY
41722D NOESY
41822D TOCSY
51912D TOCSY
52012D NOESY
52122D NOESY
52222D TOCSY
62312D TOCSY
62412D NOESY
62522D NOESY
62622D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM INSL3; 90% H2O, 10% D2090% H2O, 10% D20
21mM INSL3; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
104ambient 298 K
204ambient 303 K
304ambient 290 K
402.7ambient 298 K
505.1ambient 298 K
606.1ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3.5Brukercollection
XEASY1.3.7Bartels, C et al.data analysis
CYANA1Guntert, P. et al.structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics, cartesian dynamics / Software ordinal: 1
Details: Structure calculations and refinements were done in cns using protocols from ARIA.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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