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- PDB-1vqx: ARRESTIN-BOUND NMR STRUCTURES OF THE PHOSPHORYLATED CARBOXY-TERMI... -

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Basic information

Entry
Database: PDB / ID: 1vqx
TitleARRESTIN-BOUND NMR STRUCTURES OF THE PHOSPHORYLATED CARBOXY-TERMINAL DOMAIN OF RHODOPSIN, REFINED
ComponentsRHODOPSIN
KeywordsSIGNALING PROTEIN / HELIX-LOOP
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : ...Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / G protein-coupled opsin signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / response to light stimulus / photoreceptor outer segment / G-protein alpha-subunit binding / 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 / membrane / identical protein binding / 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 / GPCR, rhodopsin-like, 7TM ...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
AuthorsKisselev, O.G. / Downs, M.A. / Mcdowell, J.H. / Hargrave, P.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Conformational Changes in the Phosphorylated C-Terminal Domain of Rhodopsin During Rhodopsin Arrestin Interactions
Authors: Kisselev, O.G. / Downs, M.A. / Mcdowell, J.H. / Hargrave, P.A.
History
DepositionJan 7, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2005ID: 1TQK
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHODOPSIN


Theoretical massNumber of molelcules
Total (without water)2,4981
Polymers2,4981
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)15 / 100structures with the lowest energy
Representative

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Components

#1: Protein/peptide RHODOPSIN /


Mass: 2497.842 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN BOS TAURUS.
References: UniProt: P02699

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: PHOSPHATES ARE MISSING IN THIS STRUCTURE BECAUSE THEY WERE NOT PART OF THE CALCULATIONS.

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Sample preparation

DetailsContents: 0.16 MM PURIFIED ARRESTIN, 1.77 MM 7-PHOSPHO-RH(330-348) IN SODIUM PHOSPHATE BUFFER, 10% D2O IN A TOTAL VOLUME OF 0.6 ML
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: AMBIENT / Temperature: 278 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Tinker3.9PONDERrefinement
VNMR5.2structure solution
Tinker3.9structure solution
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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