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- PDB-2jnc: Refined 3D NMR structure of ECD1 of mCRF-R2beta at pH 5 -

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Basic information

Entry
Database: PDB / ID: 2jnc
TitleRefined 3D NMR structure of ECD1 of mCRF-R2beta at pH 5
ComponentsCorticotropin-releasing factor receptor 2
KeywordsLIGAND BINDING PROTEIN / SCR fold / Elliptical b-sandwich
Function / homology
Function and homology information


gastric motility / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / corticotropin-releasing hormone receptor activity / corticotrophin-releasing factor receptor activity / negative regulation of follicle-stimulating hormone secretion / negative regulation of luteinizing hormone secretion / negative regulation of norepinephrine secretion / positive regulation of serotonin secretion ...gastric motility / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / corticotropin-releasing hormone receptor activity / corticotrophin-releasing factor receptor activity / negative regulation of follicle-stimulating hormone secretion / negative regulation of luteinizing hormone secretion / negative regulation of norepinephrine secretion / positive regulation of serotonin secretion / G alpha (s) signalling events / negative regulation of epinephrine secretion / catecholamine biosynthetic process / varicosity / positive regulation of stress-activated MAPK cascade / negative regulation of calcium ion import / cell body fiber / 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 / positive regulation of cAMP-mediated signaling / axon terminus / epithelial cell differentiation / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / actin filament organization / long-term synaptic potentiation / 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 / torsion angle dynamics, molecular dynamics
Model detailsRefined structure with the PDB code 1U34 at pH 7.4
AuthorsGrace, C.R.R. / Perrin, M.H. / Jozsef, G. / DiGruccio, M.R. / Cantle, J.P. / Rivier, J.E. / Vale, W.W. / Riek, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure of the N-terminal domain of a type B1 G protein-coupled receptor in complex with a peptide ligand
Authors: Grace, C.R.R. / Perrin, M.H. / Jozsef, G. / DiGruccio, M.R. / Cantle, J.P. / Rivier, J.E. / Vale, W.W. / Riek, R.
History
DepositionJan 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Corticotropin-releasing factor receptor 2


Theoretical massNumber of molelcules
Total (without water)13,6441
Polymers13,6441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Corticotropin-releasing factor receptor 2 / CRF-R 2 / CRF2 / Corticotropin-releasing hormone receptor 2 / CRH-R 2 / CRF-RB / CRH- R2


Mass: 13644.091 Da / Num. of mol.: 1 / Fragment: residues 39-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crhr2, Crf2r / Production host: Escherichia coli (E. coli) / References: UniProt: Q60748

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Refined structure with the PDB code 1U34 at pH 7.4
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D (H)CCH-TOCSY
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1612D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.3 mM [U-100% 13C, U-100% 15N] ECD1-CRF-R2beta, 10 mM BisTris(Hcl), 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.3 mM / Component: ECD1 of mCRF-R2 beta / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303.15 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readenergy minimization
MOLMOLKoradi, Billeter and Wuthrichmolecule viewing and analysis
CYANA1.0.6Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1069 / NOE intraresidue total count: 1069
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 6.5 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 2.4 Å / Maximum torsion angle constraint violation: 10.7 ° / Maximum upper distance constraint violation: 7 Å / Torsion angle constraint violation method: GRIDSEARCH

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