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- PDB-1ln6: STRUCTURE OF BOVINE RHODOPSIN (Metarhodopsin II) -

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Basic information

Entry
Database: PDB / ID: 1ln6
TitleSTRUCTURE OF BOVINE RHODOPSIN (Metarhodopsin II)
ComponentsRHODOPSIN
KeywordsMEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTOR / METARHODOPSIN II / RHODOPSIN
Function / homology
Function and homology information


Activation of the phototransduction cascade / The canonical retinoid cycle in rods (twilight vision) / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (i) signalling events / Opsins / VxPx cargo-targeting to cilium / G protein-coupled receptor complex / opsin binding / photoreceptor inner segment membrane / absorption of visible light ...Activation of the phototransduction cascade / The canonical retinoid cycle in rods (twilight vision) / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (i) signalling events / Opsins / VxPx cargo-targeting to cilium / G protein-coupled receptor complex / opsin binding / photoreceptor inner segment membrane / absorption of visible light / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / phototransduction, visible light / arrestin family protein binding / rhodopsin mediated signaling pathway / photoreceptor cell maintenance / photoreceptor outer segment membrane / photoreceptor disc membrane / outer membrane / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / phototransduction / guanyl-nucleotide exchange factor activity / retina development in camera-type eye / visual perception / protein-chromophore linkage / cell-cell junction / Golgi membrane / G protein-coupled receptor signaling pathway / protein phosphorylation / integral component of plasma membrane / zinc ion binding / integral component of membrane / identical protein binding / plasma membrane
Rhodopsin, N-terminal / Visual pigments (opsins) retinal binding site. / Amino terminal of the G-protein receptor rhodopsin / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 signature. / Rhodopsin / Opsin / GPCR, rhodopsin-like, 7TM ...Rhodopsin, N-terminal / Visual pigments (opsins) retinal binding site. / Amino terminal of the G-protein receptor rhodopsin / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / G-protein coupled receptors family 1 signature. / Rhodopsin / Opsin / GPCR, rhodopsin-like, 7TM / Visual pigments (opsins) retinal binding site / Rhodopsin 7-helix transmembrane proteins / Rhopdopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Rhodopsin
MethodSOLUTION NMR / MULTI-DIMENSIONAL NMR,CD, SIMULATED ANNEALING WITH MMFF94 FORCE FIELD, MOLECULAR DYNAMICS WITH CHARMM FORCE FIELD
AuthorsChoi, G. / Landin, J. / Galan, J.F. / Birge, R.R. / Albert, A.D. / Yeagle, P.L.
CitationJournal: Biochemistry / Year: 2002
Title: Structural studies of metarhodopsin II, the activated form of the G-protein coupled receptor, rhodopsin.
Authors: Choi, G. / Landin, J. / Galan, J.F. / Birge, R.R. / Albert, A.D. / Yeagle, P.L.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHODOPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3162
Polymers39,0311
Non-polymers2841
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10structures with the lowest energy
Representative

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Components

#1: Protein/peptide RHODOPSIN /


Mass: 39031.457 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This protein was chemically synthesized using a SOLID STATE PEPTIDE SYNTHESIZER. It is naturally found in Bos taurus (bovine)
References: UniProt: P02699
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Retinal

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
12D NOESY
2DQF-COSY

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Sample preparation

DetailsContents: FRAGMENTS OF RHODOPSIN / Solvent system: D2O, DMSO, DPC MICELLES
Sample conditionsIonic strength: 10 mM / pH: 6.00 / Pressure: 1 atm / Temperature: 283.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software

Developer: TRIPOS / Name: SYBYL / Version: 6.6

Classification
refinement
structure solution
RefinementMethod: MULTI-DIMENSIONAL NMR,CD, SIMULATED ANNEALING WITH MMFF94 FORCE FIELD, MOLECULAR DYNAMICS WITH CHARMM FORCE FIELD
Software ordinal: 1
Details: SECONDARY STRUCTURE FROM NMR STRUCTURES OF PEPTIDES ENCODING HELICES OR TURNS, AND LONG-RANGE DISTANCE CONSTRAINTS FROM OTHER MEASUREMENTS ON INTACT PROTEIN AMINO TERMINUS REMOVED DUE TO LACK OF LONG-RANGE CONSTRAINTS
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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