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- PDB-1lvz: METARHODOPSIN II BOUND STRUCTURE OF C-TERMINAL PEPTIDE OF ALPHA-S... -

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Basic information

Entry
Database: PDB / ID: 1lvz
TitleMETARHODOPSIN II BOUND STRUCTURE OF C-TERMINAL PEPTIDE OF ALPHA-SUBUNIT OF TRANSDUCIN
ComponentsGuanine nucleotide-binding protein G(T), alpha-1 subunit
KeywordsPEPTIDE BINDING PROTEIN / alpha helix / rhodopsin-transducin complex
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment ...negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment / visual perception / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / GTP binding / protein kinase binding / metal ion binding
Similarity search - Function
G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(t) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsKoenig, B.W. / Kontaxis, G. / Mitchell, D.C. / Louis, J.M. / Litman, B.J. / Bax, A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure and orientation of a G protein fragment in the receptor bound state from residual dipolar couplings.
Authors: Koenig, B.W. / Kontaxis, G. / Mitchell, D.C. / Louis, J.M. / Litman, B.J. / Bax, A.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX Determination Method: Author Determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(T), alpha-1 subunit


Theoretical massNumber of molelcules
Total (without water)1,2931
Polymers1,2931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy structure

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Components

#1: Protein/peptide Guanine nucleotide-binding protein G(T), alpha-1 subunit / Transducin alpha-1 chain


Mass: 1293.470 Da / Num. of mol.: 1 / Fragment: S2 Peptide, Residues 339-349 / Mutation: K340R, C346S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAT1 / Plasmid: GEV-S2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04695

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D 1H-15N HSQC (w/o 1H decoupling)
1322D 1H-13C CT-HSQC (w/o 1H decoupling)
NMR detailsText: sample was studied in dark adapted state and after photo activation of rhodopsin by illuminating the sample for 60s with a focussed microscope light, chemical shifts of S2 peptide are identical ...Text: sample was studied in dark adapted state and after photo activation of rhodopsin by illuminating the sample for 60s with a focussed microscope light, chemical shifts of S2 peptide are identical in both states, TrNOEs and TrDCs are difference values between the dark and light-activated states. orientation of the bound peptide relative to the membrane normal was determined from residual dipolar couplings. the membrane normal that belongs to model 1 runs parallel to the y-axis of the coordinate frame in which the deposited s2 peptide coordinates are specified.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.6mM S2 peptide U-15N, 0.063mM rhodopsin as part of intact disk membranes from bovine retina; buffer: 10 mM HEPES, 20mM KCl, 0.05mM DTPA90% H2O/10% D2O
22.6mM S2 peptide U-15N, 13C, 0.063mM rhodopsin as part of intact disk membranes from bovine retina; buffer: 10 mM HEPES, 20mM KCl, 0.05mM DTPA90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM HEPES, 20 mM KCl / pH: 6.6 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
X-PLORNIHA.T. Brungerstructure solution
X-PLORNIHA.T. Brunger, N. Tjandra, C.D. Schwieters, J. Kuszewski, G.M. Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 121 NOE-derived distance constraints, 12 NOE-derived dihedral angle restraints, and 38 residual dipolar couplings
NMR representativeSelection criteria: lowest energy structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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