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- PDB-1got: HETEROTRIMERIC COMPLEX OF A GT-ALPHA/GI-ALPHA CHIMERA AND THE GT-... -

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Basic information

Entry
Database: PDB / ID: 1got
TitleHETEROTRIMERIC COMPLEX OF A GT-ALPHA/GI-ALPHA CHIMERA AND THE GT-BETA-GAMMA SUBUNITS
Components
  • GT-ALPHA/GI-ALPHA CHIMERA
  • GT-BETA
  • GT-GAMMA
KeywordsCOMPLEX (GTP-BINDING/TRANSDUCER) / COMPLEX (GTP-BINDING-TRANSDUCER) / G PROTEIN / HETEROTRIMER SIGNAL TRANSDUCTION / COMPLEX (GTP-BINDING-TRANSDUCER) complex
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / detection of light stimulus involved in visual perception / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels ...negative regulation of cyclic-nucleotide phosphodiesterase activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / detection of light stimulus involved in visual perception / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / G protein-coupled receptor complex / 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 / photoreceptor outer segment membrane / 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 / acyl binding / phototransduction, visible light / response to light stimulus / phototransduction / photoreceptor inner segment / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / photoreceptor disc membrane / GDP binding / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / intracellular protein localization / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / synapse / protein-containing complex binding / protein kinase binding / GTP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Few Secondary Structures / Irregular / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / P-loop containing nucleotide triphosphate hydrolases / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Guanine nucleotide-binding protein G(t) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsLambright, D.G. / Sondek, J. / Bohm, A. / Skiba, N.P. / Hamm, H.E. / Sigler, P.B.
Citation
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.
#1: Journal: Nature / Year: 1996
Title: Crystal Structure of a Ga Protein Beta Gamma Dimer at 2.1A Resolution
Authors: Sondek, J. / Bohm, A. / Lambright, D.G. / 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
DepositionAug 7, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GT-ALPHA/GI-ALPHA CHIMERA
B: GT-BETA
G: GT-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1384
Polymers86,6953
Non-polymers4431
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-53 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.400, 91.400, 83.200
Angle α, β, γ (deg.)90.00, 120.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-356-

HOH

21G-357-

HOH

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Components

#1: Protein GT-ALPHA/GI-ALPHA CHIMERA


Mass: 40685.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS IS A CHIMERIC PROTEIN WHERE RESIDUES 216-294 OF BOVINE GT ALPHA HAVE BEEN REPLACED WITH RESIDUES 220-298 OF RAT GI ALPHA 1
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: RETINA / Description: T7 LAC PROMOTER / Cell: ROD / Fragment: 216 - 294 / Organ: EYE / Organelle: ROD OUTER SEGMENT / Plasmid: PET VECTOR / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P04695
#2: Protein GT-BETA / BETA1 / TRANSDUCIN BETA SUBUNIT


Mass: 37430.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: RETINA / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / References: UniProt: P62871
#3: Protein GT-GAMMA / GAMMA1 / TRANSDUCIN GAMMA SUBUNIT


Mass: 8578.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GT-BETA-GAMMA WAS TREATED WITH ENDOPROTEASE-LYSC TO REMOVE THE THREE C-TERMINAL AMINO ACIDS AND THE TERMINAL FARNESYL MOIETY OF GAMMA
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: RETINA / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / References: UniProt: P02698
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsGT-BETA-GAMMA WAS TREATED WITH ENDOPROTEASE-LYSC TO REMOVE THE THREE C-TERMINAL AMINO ACIDS AND THE ...GT-BETA-GAMMA WAS TREATED WITH ENDOPROTEASE-LYSC TO REMOVE THE THREE C-TERMINAL AMINO ACIDS AND THE FARNESYL MOIETY OF THE GAMMA SUBUNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 MG/ML OF HETEROTRIMERIC COMPLEX WERE MIXED 1:1 WITH WELL SOLUTION CONTAINING 10% PEG-8000, 50 MM TRIS, PH 8.0, 10% GLYCEROL, 50 MM NACL, .1 MM MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS ...Details: 10 MG/ML OF HETEROTRIMERIC COMPLEX WERE MIXED 1:1 WITH WELL SOLUTION CONTAINING 10% PEG-8000, 50 MM TRIS, PH 8.0, 10% GLYCEROL, 50 MM NACL, .1 MM MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS WELL SOLUTION IN HANGING DROPS AT 4 DEGREES C., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 %PEG80001drop
350 mMTris-HCl1drop
410 %glycerol1drop
550 mM1dropNaCl
60.1 %beta-mercaptoethanol1drop
710 %PEG80001reservoir
850 mMTris-HCl1reservoir
910 %glycerol1reservoir
1050 mM1reservoirNaCl
1110 %beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 54174 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
SHELXSphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.295 -10 %
Rwork0.207 --
obs0.207 54174 99 %
Displacement parametersBiso mean: 30.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.02 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5803 0 28 616 6447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
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
Num. reflection all: 54174 / Num. reflection obs: 49438 / Rfactor all: 0.207 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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