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- PDB-2k6u: The Solution Structure of a Conformationally Restricted Fully Act... -

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Basic information

Entry
Database: PDB / ID: 2k6u
TitleThe Solution Structure of a Conformationally Restricted Fully Active Derivative of the Human Relaxin-like Factor (RLF)
Components
  • Insulin-like 3 A chain
  • Insulin-like 3 B chain
KeywordsHORMONE / protein / cross-link / isopeptide / Cleavage on pair of basic residues / Disease mutation / Polymorphism / Secreted
Function / homology
Function and homology information


Relaxin receptors / oocyte maturation / positive regulation of wound healing / positive regulation of epithelial cell migration / positive regulation of cAMP-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor binding / insulin receptor binding / hormone activity / male gonad development ...Relaxin receptors / oocyte maturation / positive regulation of wound healing / positive regulation of epithelial cell migration / positive regulation of cAMP-mediated signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor binding / insulin receptor binding / hormone activity / male gonad development / cell-cell signaling / G alpha (s) signalling events / spermatogenesis / protease binding / negative regulation of cell population proliferation / signaling receptor binding / 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/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
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsBullesbach, E.E. / Hass, M.A.S. / Jensen, M.R. / Hansen, D.F. / Kristensen, S.M. / Schwabe, C. / Led, J.J.
CitationJournal: Biochemistry / Year: 2008
Title: Solution structure of a conformationally restricted fully active derivative of the human relaxin-like factor
Authors: Bullesbach, E.E. / Hass, M.A.S. / Jensen, M.R. / Hansen, D.F. / Kristensen, S.M. / Schwabe, C. / Led, J.J.
History
DepositionJul 24, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,9472
Polymers5,9472
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Insulin-like 3 A chain / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor / RLF


Mass: 2835.240 Da / Num. of mol.: 1 / Fragment: UNP residues 106-131 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P51460
#2: Protein/peptide Insulin-like 3 B chain / Leydig insulin-like peptide / Ley-I-L / Relaxin-like factor / RLF


Mass: 3111.731 Da / Num. of mol.: 1 / Fragment: UNP residues 25-51 / Mutation: R50K / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P51460

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
4122D DQF-COSY
4222D 1H-1H TOCSY
4322D 1H-1H TOCSY
4422D 1H-13C HSQC
4522D 1H-1H NOESY
3612D 1H-1H TOCSY
3712D 1H-1H NOESY
2812D 1H-1H NOESY
1912D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM RLF_crosslinked; sodium acetate, 92% H2O/8% D2O92% H2O/8% D2O
21.2 mM RLF_crosslinked; sodium acetate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.2 mMRLF_crosslinked; sodium acetate1
1.2 mMRLF_crosslinked; sodium acetate2
Sample conditions
Conditions-IDpHTemperature (K)
15.0 298 K
25.0 303 K
35.0 308 K
4308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesnoe assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PREDITORWishartbond angle prediction
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1050 / NOE intraresidue total count: 457 / NOE long range total count: 182 / NOE medium range total count: 188 / NOE sequential total count: 223
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 6 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.048 Å / Distance rms dev error: 0.0075 Å

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