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- PDB-1nzs: NMR structures of phosphorylated carboxy terminus of bovine rhodo... -

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Basic information

Entry
Database: PDB / ID: 1nzs
TitleNMR structures of phosphorylated carboxy terminus of bovine rhodopsin in arrestin-bound state
Components19-mer peptide fragment of RHODOPSIN
KeywordsSIGNALING PROTEIN / rhodopsin / GPCR / arrestin / phosphorylation / helix-loop / ball-and-chain / bound conformation / signal termination
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction, visible light / G-protein alpha-subunit binding / phototransduction / photoreceptor outer segment / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / 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
MethodSOLUTION NMR / distance geometry, constrained molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsKisselev, O.G. / McDowell, J.H. / Hargrave, P.A.
CitationJournal: Febs Lett. / Year: 2004
Title: The arrestin-bound conformation and dynamics of the phosphorylated carboxy-terminal region of rhodopsin.
Authors: Kisselev, O.G. / McDowell, J.H. / Hargrave, P.A.
History
DepositionFeb 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

Deposited unit
A: 19-mer peptide fragment of RHODOPSIN


Theoretical massNumber of molelcules
Total (without water)2,4981
Polymers2,4981
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)16 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide 19-mer peptide fragment of RHODOPSIN


Mass: 2497.842 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 330-348 / Mutation: all serines and threonines phosphorylated / Source method: obtained synthetically
Details: This sequence occurs naturally in Bos taurus. In a synthetic peptide, all serines and threonines are phosphorylated.
References: UniProt: P02699
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
2212D NOESY

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Sample preparation

DetailsContents: 0.16 mM of purified arrestin, 1.77 mM of 7PP, 7-phospho-Rh(330-348) or unphosphorylated Rh(330-348) in sodium phosphate buffer, 0.1 M, pH 6.5 and 10% D2O in a total volume of 0.6 ml
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1M phosphate / pH: 6.5 / Pressure: ambient / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Varian.collection
VNMR5.2Variandata analysis
Tinker3.9Ponder, J.W.structure solution
Tinker3.9Ponder, J.W.refinement
RefinementMethod: distance geometry, constrained molecular dynamics, simulated annealing
Software ordinal: 1
Details: Experimental data are for the 7-phospho-Rh(330-348) bound to arrestin. Calculations and structures submitted are without phosphate groups.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 16

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