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- PDB-1mf6: Transducin gamma subunit, C-terminal domain 60-71, rhodopsin-boun... -

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Basic information

Entry
Database: PDB / ID: 1mf6
TitleTransducin gamma subunit, C-terminal domain 60-71, rhodopsin-bound state: Ensemble of 15 models determined by TrNOE spectroscopy
ComponentsGuanine nucleotide-binding protein G(T)gamma-T1 subunit
KeywordsSIGNALING PROTEIN / G-protein / transducin / rhodopsin / GPCR / gamma subunit / bound conformation / C-terminal domain
Function / homology
Function and homology information


eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor ...eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / photoreceptor disc membrane / intracellular protein localization / G-protein beta-subunit binding / heterotrimeric G-protein complex / G protein-coupled receptor signaling pathway
Similarity search - Function
G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(T) subunit gamma-T1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / Distance geomerty, high-temperature molecular dynamics, simulated annealing
AuthorsKisselev, O.G.
CitationJournal: Structure / Year: 2003
Title: RHODOPSIN CONTROLS A CONFORMATIONAL SWITCH ON THE TRANSDUCIN gamma SUBUNIT
Authors: Kisselev, O.G. / Downs, M.A.
History
DepositionAug 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(T)gamma-T1 subunit


Theoretical massNumber of molelcules
Total (without water)1,3391
Polymers1,3391
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)15 / 15all calculated structures submitted
RepresentativeModel #1

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Components

#1: Protein/peptide Guanine nucleotide-binding protein G(T)gamma-T1 subunit / Transducin gamma chain


Mass: 1338.552 Da / Num. of mol.: 1 / Fragment: Residues 60-71
Source method: isolated from a genetically manipulated source
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in bos taurus (bovine).
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P02698

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 0.1 mM Rhodopsin, 2 mM peptide DKNPFKELKGGC-farnesyl.
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / Temperature: 277 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 spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Variancollection
VNMR5.2Variandata analysis
VNMR5.2Varianprocessing
Tinker3.9Ponder, J.W.structure solution
Tinker3.9Ponder, J.W.refinement
RefinementMethod: Distance geomerty, high-temperature molecular dynamics, simulated annealing
Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 15 / Conformers submitted total number: 15

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