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- PDB-2lsq: Analog of the fragment 197-221 of beta-1 adrenoreceptor -

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Entry
Database: PDB / ID: 2lsq
TitleAnalog of the fragment 197-221 of beta-1 adrenoreceptor
ComponentsANALOG OF THE FRAGMENT 197-221 OF BETA-1 ADRENORECEPTOR
KeywordsIMMUNE SYSTEM / beta1-adrenoreceptor / modified extracellular loop 197-221 / autoantibodies / cardiomyopathy / arrhythmia
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / positive regulation of the force of heart contraction by epinephrine-norepinephrine / beta-adrenergic receptor activity / beta1-adrenergic receptor activity / epinephrine binding / positive regulation of heart rate by epinephrine-norepinephrine / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / alpha-2A adrenergic receptor binding / regulation of circadian sleep/wake cycle, sleep / fear response ...guanyl-nucleotide exchange factor activity => GO:0005085 / positive regulation of the force of heart contraction by epinephrine-norepinephrine / beta-adrenergic receptor activity / beta1-adrenergic receptor activity / epinephrine binding / positive regulation of heart rate by epinephrine-norepinephrine / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / alpha-2A adrenergic receptor binding / regulation of circadian sleep/wake cycle, sleep / fear response / norepinephrine binding / Adrenoceptors / heat generation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of multicellular organism growth / diet induced thermogenesis / plasma membrane => GO:0005886 / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / response to cold / positive regulation of GTPase activity / G protein-coupled receptor activity / PDZ domain binding / Schaffer collateral - CA1 synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of cold-induced thermogenesis / G alpha (s) signalling events / early endosome / G protein-coupled receptor signaling pathway / protein heterodimerization activity / plasma membrane
Similarity search - Function
Beta 1 adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 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
Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBushuev, V.N. / Zykov, K.A. / Bespalova, Z.D. / Bibilashvili, R.S. / Efremov, E.E. / Golitsyn, S.P. / Kaznacheeva, L.I. / Kuzhetsova, T.V. / Levashov, P.S. / Masenko, V.P. ...Bushuev, V.N. / Zykov, K.A. / Bespalova, Z.D. / Bibilashvili, R.S. / Efremov, E.E. / Golitsyn, S.P. / Kaznacheeva, L.I. / Kuzhetsova, T.V. / Levashov, P.S. / Masenko, V.P. / Mironova, N.A. / Molokoedov, F.S. / Rutkevich, P.N. / Rvacheva, A.V. / Sharf, T.V. / Sidorova, M.V. / Vlasik, T.N. / Yanushevskaya, E.V.
CitationJournal: To be Published
Title: Analog of the fragment 197-221 of 1-adrenoreceptor
Authors: Bushuev, V.N.
History
DepositionMay 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Assembly

Deposited unit
A: ANALOG OF THE FRAGMENT 197-221 OF BETA-1 ADRENORECEPTOR


Theoretical massNumber of molelcules
Total (without water)2,9411
Polymers2,9411
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide ANALOG OF THE FRAGMENT 197-221 OF BETA-1 ADRENORECEPTOR / Beta-1 adrenoreceptor / Beta-1 adrenoceptor


Mass: 2941.242 Da / Num. of mol.: 1 / Fragment: Extracellular Topological domain / Source method: obtained synthetically
Details: The peptide was prepared by automatic solid phase synthesis (SPPS) using the Fmoc strategy starting from 0.25 mmol of commercial N Fmoc-Lys(Boc)-polymer (Bachem, Switzerland). A copolymer of ...Details: The peptide was prepared by automatic solid phase synthesis (SPPS) using the Fmoc strategy starting from 0.25 mmol of commercial N Fmoc-Lys(Boc)-polymer (Bachem, Switzerland). A copolymer of styrene with 1% divinylbenzene with a hydroxymethylphenyloxymethyl anchoring group (the Wang-polymer) was used as a carrier. The side functions of the amino acids were blocked by the following protective groups: But for hydroxyl functions of Ser and Tyr; But for carboxyl functions of Asp and Glu; Boc for -amino functions of Lys; Trt for carboxylamide group of Asn, sulfhydryl functions of residues Cys198 and Cys220; Acm for sulfhydryl functions of residues Cys209 and Cys215, and Pbf for guanidine function of Arg. The amino acid chain was elongated stepwise starting from C-terminus using carbodiimide in the presence of 1-hydroxybenzotriasole. When the SPPS was finished, the peptide was cleaved from carrier with the simultaneous removal of the acid-labile protective groups by treatment with trifluoracetic acid with the addition of water, triisopropylsilane and dithiothreitole. The synthesized [Cys(Acm)2]peptide was purified by HPLC to a purity 85-90%. The intramolecular S-S bridge between Cys198 and Cys220 was with hydrogen peroxide at pH 8. The target monocyclic intermediate of peptide was purified by HPLC to a purity 90-95%. The product was characterized by MALDI-TOF mass spectrometry. The second disulfide bond between Cys209 and Cys215 was formed by the treatment of monocyclic intermediate [Cys(Acm)2]peptide with iodine (for simultaneous cleavage of Acm group and formation S-S bridge) in methanol. The bicyclic target product was purified by HPLC to a purity 98% and characterized by MALDI-TOF mass spectrometry.
Source: (synth.) Homo sapiens (human) / References: UniProt: P08588
Sequence detailsAUTHORS STATE THAT THIS IS AN ANALOG OF THE FRAGMENT 197-221 OF BETA-1 ADRENORECEPTOR.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Analog of the fragment 197-221 of 1- adrenoreceptor
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-13C HSQC aliphatic
1222D 1H-13C HSQC aromatic
1322D DQF-COSY
1422D 1H-1H NOESY
1522D 1H-1H TOCSY
1612D 1H-1H NOESY
1712D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM protein, 1 mM sodium azide, 20 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
22 mM protein, 1 mM sodium azide, 20 mM [U-100% 2H] sodium acetate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-11
1 mMsodium azide-21
20 mMsodium acetate-3[U-100% 2H]1
2 mMentity-42
1 mMsodium azide-52
20 mMsodium acetate-6[U-100% 2H]2
Sample conditionsIonic strength: 22 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DPX / Manufacturer: Bruker / Model: DPX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Bruker Biospincollection
XwinNMR1.3Bruker Biospinprocessing
CARA1.9.5Keller and Wuthrichchemical shift assignment
CARA1.9.5Keller and Wuthrichpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 182 / NOE intraresidue total count: 70 / NOE long range total count: 24 / NOE medium range total count: 28 / NOE sequential total count: 60
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 1.3 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum torsion angle constraint violation: 8 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.05 Å

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