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- PDB-1u34: 3D NMR structure of the first extracellular domain of CRFR-2beta,... -

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Basic information

Entry
Database: PDB / ID: 1u34
Title3D NMR structure of the first extracellular domain of CRFR-2beta, a type B1 G-protein coupled receptor
ComponentsCorticotropin releasing factor receptor 2
KeywordsSIGNALING PROTEIN / Beta sheets and Loops
Function / homology
Function and homology information


gastric motility / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity / negative regulation of follicle-stimulating hormone secretion / negative regulation of norepinephrine secretion / positive regulation of serotonin secretion / negative regulation of luteinizing hormone secretion ...gastric motility / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / corticotrophin-releasing factor receptor activity / corticotropin-releasing hormone receptor activity / negative regulation of follicle-stimulating hormone secretion / negative regulation of norepinephrine secretion / positive regulation of serotonin secretion / negative regulation of luteinizing hormone secretion / G alpha (s) signalling events / negative regulation of epinephrine secretion / catecholamine biosynthetic process / varicosity / negative regulation of calcium ion import / cell body fiber / positive regulation of cAMP-mediated signaling / positive regulation of stress-activated MAPK cascade / positive regulation of blood pressure / protein kinase C-activating G protein-coupled receptor signaling pathway / G protein-coupled peptide receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of DNA biosynthetic process / positive regulation of heart rate / negative regulation of feeding behavior / peptide hormone binding / axon terminus / epithelial cell differentiation / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / long-term synaptic potentiation / actin filament organization / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / hormone activity / positive regulation of interleukin-6 production / perikaryon / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / axon / negative regulation of gene expression / neuronal cell body / dendrite / positive regulation of gene expression / plasma membrane
Similarity search - Function
GPCR, family 2, corticotropin releasing factor receptor, type 2 / GPCR, family 2, corticotropin releasing factor receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily ...GPCR, family 2, corticotropin releasing factor receptor, type 2 / GPCR, family 2, corticotropin releasing factor receptor / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Corticotropin-releasing factor receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsGrace, C.R. / Perrin, M.H. / DiGruccio, M.R. / Miller, C.L. / Rivier, J.E. / Vale, W.W. / Riek, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: NMR structure and peptide hormone binding site of the first extracellular domain of a type B1 G protein-coupled receptor
Authors: Grace, C.R. / Perrin, M.H. / DiGruccio, M.R. / Miller, C.L. / Rivier, J.E. / Vale, W.W. / Riek, R.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Corticotropin releasing factor receptor 2


Theoretical massNumber of molelcules
Total (without water)13,6261
Polymers13,6261
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 / 100structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein Corticotropin releasing factor receptor 2 / CRFR2b


Mass: 13626.097 Da / Num. of mol.: 1 / Fragment: ECD1 of CRFR2b
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q60748

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNCA-J
1413D CBCA(CO)NH
1522D TOCSY
1622D NOESY
NMR detailsText: The NOEs for structure calculation were taken from 3D and 2D NOESY experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM 13C, 15N labelled ECD1-CRFR2b in 10mM BisTris(HCl); pH 7.495% H2O/5% D2O
20.2mM 13C, 15N labelled ECD1-CRFR2b in 10mM BisTris(HCl); pH 7.4100% D2O
Sample conditionsIonic strength: 0.2mM in 10mM BisTris(HCl) / pH: 7.4 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Peter Guntert, Torsten Herrmannstructure solution
CYANA1.0.6Peter Guntert, Torsten Herrmannrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: A total of 1089 meaningful distance restraints and 362 angle restraints were used as an input in the program CYANA followed by restrained energy minimisation using INSIGHT.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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