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- PDB-2m96: Solution NMR structure of the RXFP2 LDLa module -

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Basic information

Entry
Database: PDB / ID: 2m96
TitleSolution NMR structure of the RXFP2 LDLa module
ComponentsRelaxin receptor 2
KeywordsMEMBRANE PROTEIN / signaling / INSL3 receptor
Function / homology
Function and homology information


Relaxin receptors / protein-hormone receptor activity / G protein-coupled peptide receptor activity / oocyte maturation / peptide hormone binding / hormone-mediated signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / male gonad development / G alpha (s) signalling events ...Relaxin receptors / protein-hormone receptor activity / G protein-coupled peptide receptor activity / oocyte maturation / peptide hormone binding / hormone-mediated signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / male gonad development / G alpha (s) signalling events / negative regulation of cell population proliferation / negative regulation of apoptotic process / plasma membrane
Similarity search - Function
Relaxin receptor / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily ...Relaxin receptor / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Few Secondary Structures / Irregular / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsPetrie, E.J. / Gooley, P.R. / Bathgate, A.D.
CitationJournal: To be Published
Title: Solution NMR structure of the RXFP2 LDLa module
Authors: Petrie, E.J. / Gooley, P.R. / Bathgate, A.D.
History
DepositionJun 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Relaxin receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6862
Polymers4,6461
Non-polymers401
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Relaxin receptor 2 / G-protein coupled receptor 106 / G-protein coupled receptor affecting testicular descent / Leucine- ...G-protein coupled receptor 106 / G-protein coupled receptor affecting testicular descent / Leucine-rich repeat-containing G-protein coupled receptor 8 / Relaxin family peptide receptor 2


Mass: 4646.184 Da / Num. of mol.: 1 / Fragment: LDL-receptor class A domain residues 38-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXFP2, GPR106, GREAT, LGR8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXD0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D C(CO)NH
1423D 1H-13C NOESY
1513D HBHA(CO)NH
1613D H(CCO)NH
1723D (H)CCH-TOCSY
1823D HN(CA)CB
1913D HNCO
11013D HNHB
11132D 1H-1H NOESY
11232D 1H-1H TOCSY
11313D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM [U-99% 15N] protein, 50 mM imidazole, 10 mM CALCIUM ION, 90% H2O/10% D2O90% H2O/10% D2O
22.5 mM [U-99% 13C; U-99% 15N] protein, 50 mM imidazole, 10 mM CALCIUM ION, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM protein, 50 mM [U-2H] imidazole, 10 mM CALCIUM ION, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMentity_1-1[U-99% 15N]1
50 mMimidazole-21
10 mMCALCIUM ION-31
2.5 mMentity_1-4[U-99% 13C; U-99% 15N]2
50 mMimidazole-52
10 mMCALCIUM ION-62
0.5 mMentity_1-73
50 mMimidazole-8[U-2H]3
10 mMCALCIUM ION-93
Sample conditionsIonic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ccpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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