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- PDB-1gp2: G PROTEIN HETEROTRIMER GI_ALPHA_1 BETA_1 GAMMA_2 WITH GDP BOUND -

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Basic information

Entry
Database: PDB / ID: 1gp2
TitleG PROTEIN HETEROTRIMER GI_ALPHA_1 BETA_1 GAMMA_2 WITH GDP BOUND
Components
  • G PROTEIN GI ALPHA 1
  • G PROTEIN GI BETA 1
  • G PROTEIN GI GAMMA 2
KeywordsCOMPLEX (GTP-BINDING/TRANSDUCER) / SIGNAL TRANSDUCTION PROTEIN / GTPASE / WD40 / RAS-LIKE / COMPLEX (GTP-BINDING-TRANSDUCER) / COMPLEX (GTP-BINDING-TRANSDUCER) complex
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / negative regulation of synaptic transmission / GTPase activating protein binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / negative regulation of synaptic transmission / GTPase activating protein binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / 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 / neurotransmitter receptor localization to postsynaptic specialization 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 / positive regulation of protein localization to cell cortex / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / regulation of mitotic spindle organization / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / G protein activity / GTPase binding / retina development in camera-type eye / midbody / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / synapse / centrosome / protein-containing complex binding / GTP binding / glutamatergic synapse / magnesium ion binding / protein-containing complex / nucleus / membrane / plasma membrane / cytosol / 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(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsWall, M.A. / Sprang, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2.
Authors: Wall, M.A. / Coleman, D.E. / Lee, E. / Iniguez-Lluhi, J.A. / Posner, B.A. / Gilman, A.G. / Sprang, S.R.
History
DepositionNov 13, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: G PROTEIN GI ALPHA 1
B: G PROTEIN GI BETA 1
G: G PROTEIN GI GAMMA 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9734
Polymers85,5303
Non-polymers4431
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-61 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.289, 84.289, 132.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein G PROTEIN GI ALPHA 1


Mass: 40267.836 Da / Num. of mol.: 1 / Fragment: ALPHA 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: SF9 / Production host: Escherichia coli (E. coli) / Strain (production host): SF9 / References: UniProt: P10824
#2: Protein G PROTEIN GI BETA 1


Mass: 37416.930 Da / Num. of mol.: 1 / Fragment: BETA 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: SF9 / References: UniProt: P62871
#3: Protein G PROTEIN GI GAMMA 2


Mass: 7845.078 Da / Num. of mol.: 1 / Fragment: GAMMA 2 / Mutation: CHAIN G, C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: BOVINE BETA 1 AND GAMMA 2 WERE COEXPRESSED IN SF9 CELLS INFECTED WITH RECOMBINANT BACULOVIRUSES AND PURIFIED AS A COMPLEX
Cell line: SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P63212
#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.: 390 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %PEG80001reservoir
2100 mMNa-HEPES1reservoirpH7.0
3100 mMsodium acetate1reservoirpH6.4
40.05 %n-beta-octyl-glucoside1reservoir
52 %2-propanol1reservoir
67.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Date: Mar 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 36822 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 2.23 / % possible all: 62

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 1
Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 3653 10 %RANDOM
Rwork0.226 ---
obs0.226 36701 89.8 %-
Displacement parametersBiso mean: 68.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 28 0 390 6195
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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