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- PDB-1tbg: BETA-GAMMA DIMER OF THE HETEROTRIMERIC G-PROTEIN TRANSDUCIN -

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Basic information

Entry
Database: PDB / ID: 1tbg
TitleBETA-GAMMA DIMER OF THE HETEROTRIMERIC G-PROTEIN TRANSDUCIN
Components(TRANSDUCIN) x 2
KeywordsCOMPLEX (GTP-BINDING/TRANSDUCER) / COMPLEX (GTP-BINDING-TRANSDUCER) / EYE / TRANSDUCER / PRENYLATION / COMPLEX (GTP-BINDING-TRANSDUCER) complex
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / 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 ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / 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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / G protein-coupled receptor signaling pathway / membrane / cytoplasm
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Few Secondary Structures / Irregular / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSondek, J.S. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B.
Citation
Journal: Nature / Year: 1996
Title: Crystal structure of a G-protein beta gamma dimer at 2.1A resolution.
Authors: Sondek, J. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B.
#1: Journal: Nature / Year: 1996
Title: The 2.0 A Crystal Structure of a Heterotrimeric G Protein
Authors: Lambright, D.G. / Sondek, J. / Bohm, A. / Skiba, N.P. / Hamm, H.E. / Sigler, P.B.
#2: Journal: Nature / Year: 1994
Title: Structural Determinants for Activation of the Alpha-Subunit of a Heterotrimeric G Protein
Authors: Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B.
#3: Journal: Nature / Year: 1994
Title: Gtpase Mechanism of Gproteins from the 1.7-A Crystal Structure of Transducin Alpha-Gdp-Aif-4
Authors: Sondek, J. / Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B.
#4: Journal: Nature / Year: 1993
Title: The 2.2 A Crystal Structure of Transducin-Alpha Complexed with GTP Gamma S
Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B.
History
DepositionJun 15, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSDUCIN
E: TRANSDUCIN
B: TRANSDUCIN
F: TRANSDUCIN
C: TRANSDUCIN
G: TRANSDUCIN
D: TRANSDUCIN
H: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)181,5888
Polymers181,5888
Non-polymers00
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRANSDUCIN
G: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-43 kcal/mol
Surface area17210 Å2
MethodPISA
3
B: TRANSDUCIN
F: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-40 kcal/mol
Surface area16940 Å2
MethodPISA
4
D: TRANSDUCIN
H: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-41 kcal/mol
Surface area17070 Å2
MethodPISA
5
A: TRANSDUCIN
E: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.100, 94.000, 194.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999339, -0.035733, 0.006634), (-0.034136, 0.985506, 0.166174), (-0.012475, 0.165838, -0.986074)125.72179, -17.47346, 236.6387
2given(-0.995922, 0.021439, 0.087635), (-0.036606, -0.983829, -0.17533), (0.082459, -0.177823, 0.980602)112.69596, 114.0073, 5.20845
3given(0.993596, -0.001803, -0.112978), (0.002097, -0.999406, 0.03439), (-0.112973, -0.034407, -0.993002)13.70356, 86.21671, 252.63943

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Components

#1: Protein
TRANSDUCIN / GUANINE NUCLEOTIDE-BINDING PROTEIN G


Mass: 37416.930 Da / Num. of mol.: 4 / Fragment: BETA-1 SUBUNIT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / Tissue: RETINA / References: UniProt: P04901, UniProt: P62871*PLUS
#2: Protein
TRANSDUCIN / GUANINE NUCLEOTIDE-BINDING PROTEIN G


Mass: 7980.186 Da / Num. of mol.: 4 / Fragment: GAMMA-1 SUBUNIT / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / Tissue: RETINA / References: UniProt: P02698
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 15-20 MG/ML PROTEIN MIXED 1:1 WITH WELL SOLUTION (10MM FUMARATE, PH 4.2, 10MM MGSO4, 2MM GDCL3, 5% W/V GLYCEROL, 5% W/V PEG 4000, 15MM BETA-MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS. WELL ...Details: 15-20 MG/ML PROTEIN MIXED 1:1 WITH WELL SOLUTION (10MM FUMARATE, PH 4.2, 10MM MGSO4, 2MM GDCL3, 5% W/V GLYCEROL, 5% W/V PEG 4000, 15MM BETA-MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS. WELL SOLUTION IN HANGING DROPS AT 4 DEGREES CELSIUS., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
21 mMTris-HCl1drop
31 mM1dropMgCl2
45 mM1dropNaCl
515 mMbeta-mercaptoethanol1drop
65-7.5 %(v/v)glycerol1drop
710 mMfumarate1reservoir
810 mM1reservoirMgSO4
92 mM1reservoirGdCl3
105 %(v/v)glycerol1reservoir
115 %(v/v)PEG40001reservoir
1215 mMbeta-mercaptoethanol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 7, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionNum. obs: 88015 / % possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 258531

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.306 -
Rwork0.2 -
obs0.2 71169
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12541 0 0 732 13273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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