[English] 日本語
Yorodumi
- PDB-2jm4: The solution NMR structure of the relaxin (RXFP1) receptor LDLa m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jm4
TitleThe solution NMR structure of the relaxin (RXFP1) receptor LDLa module.
ComponentsRelaxin receptor 1
KeywordsSIGNALING PROTEIN / LDL-A module / RXFP1 receptor / LGR7
Function / homology
Function and homology information


lung connective tissue development / nipple morphogenesis / Relaxin receptors / parturition / myofibroblast differentiation / hormone binding / G protein-coupled peptide receptor activity / hormone-mediated signaling pathway / extracellular matrix organization / G protein-coupled receptor activity ...lung connective tissue development / nipple morphogenesis / Relaxin receptors / parturition / myofibroblast differentiation / hormone binding / G protein-coupled peptide receptor activity / hormone-mediated signaling pathway / extracellular matrix organization / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / metal ion binding / 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, SDS22-like subfamily / 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, torsion angle dynamics
AuthorsHopkins, E.J. / Bathgate, R.A.D. / Gooley, P.R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The NMR solution structure of the relaxin (RXFP1) receptor lipoprotein receptor class A module and identification of key residues in the N-terminal region of the module that mediate receptor activation
Authors: Hopkins, E.J. / Layfield, S. / Ferraro, T. / Bathgate, R.A.D. / Gooley, P.R.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Relaxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5762
Polymers4,5361
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 100lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Relaxin receptor 1 / Relaxin family peptide receptor 1 / Leucine-rich repeat-containing G-protein coupled receptor 7 / LDLa module


Mass: 4536.005 Da / Num. of mol.: 1 / Fragment: LDL-receptor class A, residues 23-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXFP1, LGR7 / Plasmid: pGEV-LDLa / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): trxB / References: UniProt: Q9HBX9
#2: Chemical ChemComp-CA / CALCIUM ION


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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D HNCA
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HBHA(CO)NH
1623D C(CO)NH
1723D H(CCO)NH
1812D 1H-15N HSQC
1922D 1H-15N HSQC
11023D (H)CCH-TOCSY
11113D HNHA
11213D 1H-15N NOESY
11323D 1H-13C NOESY
11413D HNHB
11523D HACAHB
11622D 1H-13C HSQC
11732D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM 15N RXFP1-LDLa, 10 mM calcium chloride, 50 mM acetic acid, 90% H2O, 10% D2O, pH 5.5 (adjusted with NaOH)sample_190% H2O/10% D2O
solution21.5 mM 13C, 15N RXFP1-LDLa, 10 mM calcium chloride, 50 mM acetic acid, 90% H2O, 10% D2O, pH 5.5 (adjusted with NaOH)sample_290% H2O/10% D2O
solution31.0 mM 10% 13C, 90% 12C RXFP1-LDLa, 10 mM calcium chloride, 50 mM acetic acid, 90% H2O, 10% D2O, pH 5.5 (adjusted with NaOH)sample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRXFP1-LDLa[U-15N]1
1.5 mMRXFP1-LDLa[U-13C; U-15N]2
1.0 mMRXFP1-LDLa[U-10% 13C]3
10 mMcalcium chloridenatural abundance1
10 mMcalcium chloridenatural abundance2
10 mMcalcium chloridenatural abundance3
50 mMacetic acidnatural abundance1
50 mMacetic acidnatural abundance2
50 mMacetic acidnatural abundance3
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 303.15 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Sparky3.106Goddarddata analysis
NMRPipe2.3Delaglio,Grzesiek,Vuister,Zhu,Pfeifer,Baxprocessing
X-PLOR NIH2.9.9Schwieters, Kuszewski, Tjandra, Clorerefinement
CYANA1.0.7Guntert,Mumenthaler,Wuthrichstructure solution
NMRView5.2.2Johnsondata analysis
ProcheckNMR3.5.4Laskowski, MacArthurrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 24 / Maximum torsion angle constraint violation: 2.7 ° / Maximum upper distance constraint violation: 0.27 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more