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- PDB-2mv1: Solution NMR structure of Human Relaxin-2 -

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Basic information

Entry
Database: PDB / ID: 2mv1
TitleSolution NMR structure of Human Relaxin-2
Components
  • Relaxin A chain
  • Relaxin B chain
KeywordsSIGNALING PROTEIN / insulin/relaxin family fold / signalling protein
Function / homology
Function and homology information


Relaxin receptors / regulation of catalytic activity / female pregnancy / hormone activity / positive regulation of angiogenesis / G alpha (s) signalling events / positive regulation of gene expression / extracellular region
Similarity search - Function
Relaxin / : / Insulin family / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHaugaard-Kedstrom, L.M. / Rosengren, K.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Solution structure, aggregation behavior, and flexibility of human relaxin-2.
Authors: Haugaard-Kedstrom, L.M. / Hossain, M.A. / Daly, N.L. / Bathgate, R.A. / Rinderknecht, E. / Wade, J.D. / Craik, D.J. / Rosengren, K.J.
History
DepositionSep 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
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_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
Revision 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Relaxin B chain
A: Relaxin A chain


Theoretical massNumber of molelcules
Total (without water)5,9732
Polymers5,9732
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Relaxin B chain


Mass: 3313.892 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Assembled by Fmoc based SPPS and combined with entity 2 using regioselective disulphide bond formation
Source: (synth.) Homo sapiens (human) / References: UniProt: P04090
#2: Protein/peptide Relaxin A chain


Mass: 2659.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Assembled by Fmoc based SPPS and combined with entity 1 using regioselective disulphide bond formation
Source: (synth.) Homo sapiens (human) / References: UniProt: P04090
Has protein modificationY

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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
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein_1, 1 mM protein_2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein_1, 1 mM protein_2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMentity_1-11
1 mMentity_2-21
1 mMentity_1-32
1 mMentity_2-42
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
TopSpin2.3Bruker Biospincollection
TopSpin2.3Bruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using Cartesian dynamics in CNS and subsequently refined and energy minimised in explicit solvent.
NMR constraintsNOE constraints total: 349 / NOE intraresidue total count: 0 / NOE long range total count: 67 / NOE medium range total count: 78 / NOE sequential total count: 204 / Hydrogen bond constraints total count: 30 / Protein chi angle constraints total count: 9 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 45 / Protein psi angle constraints total count: 35
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 torsion angle constraint violation: 2.8 ° / Maximum upper distance constraint violation: 0.3 Å

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