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- PDB-2jnd: 3D NMR structure of ECD1 of mCRF-R2b in complex with Astressin -

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Basic information

Entry
Database: PDB / ID: 2jnd
Title3D NMR structure of ECD1 of mCRF-R2b in complex with Astressin
Components
  • ASTRESSIN
  • Corticotropin-releasing factor receptor 2
KeywordsLIGAND BINDING PROTEIN / SCR fold / alpha-helix / beta-sheets
Function / homology
Function and homology information


gastric motility / corticotropin-releasing hormone receptor activity / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / 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 / corticotropin-releasing hormone receptor activity / negative regulation of defecation / Class B/2 (Secretin family receptors) / skeletal muscle tissue growth / 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 / 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 / torsion angle dynamics,distance geometry
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 1.1Jan 8, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Corticotropin-releasing factor receptor 2
B: ASTRESSIN


Theoretical massNumber of molelcules
Total (without water)17,2132
Polymers17,2132
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)19 / 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: 13626.097 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
#2: Protein/peptide ASTRESSIN


Mass: 3587.223 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide ligand is based on human CRF which is naturally found in humans.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D 1H-15N NOESY
1413D (H)CCH-TOCSY
1513D 1H-13C NOESY
1612D 1H-13C HSQC
1722D 1H-15N HSQC
1823D HNCA
1923D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY
11222D 1H-13C HSQC
11332D 1H-1H TOCSY
11432D DQF-COSY
11532D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C, U-100% 15N] ECD1-CRF-R2b-Astressin complex, 95% H2O, 5% D2O95% H2O/5% D2O
20.4 mM [U-100% 13C, U-100% 15N] ECD1-CRF-R2b-Astressin complex, 95% H2O, 5% D2O95% H2O/5% D2O
30.4 mM ECD1-CRF-R2b-Astressin complex, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMECD1-CRF-R2b-Astressin complex[U-100% 13C; U-100% 15N]1
0.4 mMECD1-CRF-R2b-Astressin complex[U-100% 13C; U-100% 15N]2
0.4 mMECD1-CRF-R2b-Astressin complex3
Sample conditionsIonic strength: 10 Bis tris / pH: 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.peak picking
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics,distance geometry / Software ordinal: 1
Details: torsion angle dynamics using CYANA, distance geometry using CNS
NMR constraintsNOE constraints total: 1524
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 10.3 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 19 / Maximum lower distance constraint violation: 3.2 Å / Maximum torsion angle constraint violation: 19.1 ° / Maximum upper distance constraint violation: 7.9 Å / Torsion angle constraint violation method: GRIDSEARCH

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