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- PDB-2kbc: Solution structure of human insulin-like peptide 5 (INSL5) -

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Basic information

Entry
Database: PDB / ID: 2kbc
TitleSolution structure of human insulin-like peptide 5 (INSL5)
Components
  • INSL5_A-chain
  • INSL5_B-chain
KeywordsHORMONE / peptide hormone / relaxin / insulin-like fold
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 / extracellular region
Similarity search - Function
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
Insulin-like peptide INSL5
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsRosengren, K.J. / Haugaard-Jonsson, L.M.
CitationJournal: Biochem.J. / Year: 2009
Title: Structure of human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework
Authors: Hossain, M.A. / Daly, N.L. / Craik, D.J. / Wade, J.D. / Rosengren, K.J.
History
DepositionNov 25, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 7, 2018Group: Derived calculations / Experimental preparation / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_exptl_sample_conditions ...pdbx_entity_src_syn / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_exptl_sample_conditions.pH / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_sample_details.contents
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_mod_residue / struct_conn / struct_ref_seq
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.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: INSL5_B-chain
A: INSL5_A-chain


Theoretical massNumber of molelcules
Total (without water)5,0512
Polymers5,0512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1390 Å2
ΔGint-12 kcal/mol
Surface area3360 Å2
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 INSL5_B-chain


Mass: 2848.372 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide chain was assembled using FMOC solid phase peptide synthesis and combined with the A-chain using regioselective disulfide bond formation
Source: (synth.) synthetic construct (others) / References: UniProt: Q9Y5Q6*PLUS
#2: Protein/peptide INSL5_A-chain


Mass: 2202.509 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide chain was assembled using FMOC solid phase peptide synthesis and combined with the B-chain using regioselective disulfide bond formation
Source: (synth.) synthetic construct (others) / References: UniProt: Q9Y5Q6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2412D 1H-1H TOCSY
2512D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.2 mM INSL5, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: INSL5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 4 ambient 298 K
20 4 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.5Keller, Wuthrichdata analysis
CYANA2Guntert, Mumenthaler, Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were generated using torsion-angle dynamics and subsequently refined and energy minimized using Cartesian dynamics and powell minimization in explicit solvent within the program CNS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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