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- PDB-2lot: AR55 solubilised in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 2lot
TitleAR55 solubilised in SDS micelles
ComponentsApelin receptor
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endocardial cushion formation ...apelin receptor activity / apelin receptor signaling pathway / regulation of gap junction assembly / positive regulation of inhibitory G protein-coupled receptor phosphorylation / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / endocardial cushion formation / adult heart development / coronary vasculature development / vasculature development / negative regulation of cAMP-mediated signaling / aorta development / ventricular septum morphogenesis / blood vessel development / heart looping / vasculogenesis / gastrulation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / G protein-coupled receptor activity / positive regulation of angiogenesis / signaling receptor activity / heart development / G alpha (i) signalling events / regulation of gene expression / angiogenesis / G protein-coupled receptor signaling pathway / negative regulation of gene expression / plasma membrane
Similarity search - Function
MYOD Basic-Helix-Loop-Helix Domain, subunit B - #20 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Apelin receptor / Other non-globular / Special / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsExtended conformation, model 15
AuthorsLangelaan, D.N. / Rainey, J.K.
CitationJournal: J Phys Chem Lett / Year: 2017
Title: Preserved Transmembrane Segment Topology, Structure, and Dynamics in Disparate Micellar Environments.
Authors: Langelaan, D.N. / Pandey, A. / Sarker, M. / Rainey, J.K.
History
DepositionJan 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apelin receptor


Theoretical massNumber of molelcules
Total (without water)7,3061
Polymers7,3061
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)40 / 100structures with the lowest energy
RepresentativeModel #1extended conformation

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Components

#1: Protein Apelin receptor / / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11


Mass: 7306.109 Da / Num. of mol.: 1 / Fragment: UNP residues 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLNR, AGTRL1, APJ / Production host: Escherichia coli (E. coli) / References: UniProt: P35414

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CO)CA
131HN(CA)CO (H[N[ca[CO]]])
1413D HNCA
1513D HN(CA)CB
161HN(CO)CACB (H[N[co[{CA|ca[C]}]]])
17113CHSQC (H[{N|C}])
1812D 1H-15N HSQC/HMQC
1913D 1H-15N TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.8 mM [U-99% 13C; U-99% 15N] AR55, 96 mM [U-99% 2H] SDS, 20 mM sodium acetate, 1 mM sodium azide, 1 mM DSS, 10 mM [U-99% 2H] DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMAR55-1[U-99% 13C; U-99% 15N]1
96 mMSDS-2[U-99% 2H]1
20 mMsodium acetate-31
1 mMsodium azide-41
1 mMDSS-51
10 mMDTT-6[U-99% 2H]1
Sample conditionspH: 5 / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: extended conformation
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

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