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- PDB-1git: STRUCTURE OF GTP-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1git
TitleSTRUCTURE OF GTP-BINDING PROTEIN
ComponentsG PROTEIN GI ALPHA 1
KeywordsGTP-BINDING PROTEIN / GTP-ASE / TRANSDUCER / ADENYLATE CYCLASE / MULTIGENE FAMILY / MYRISTYLATION
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of protein localization to cell cortex / T cell migration ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / GDP binding / heterotrimeric G-protein complex / G protein activity / midbody / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / glutamatergic synapse / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBerghuis, A.M. / Lee, E. / Sprang, S.R.
Citation
Journal: Structure / Year: 1996
Title: Structure of the GDP-Pi complex of Gly203-->Ala gialpha1: a mimic of the ternary product complex of galpha-catalyzed GTP hydrolysis.
Authors: Berghuis, A.M. / Lee, E. / Raw, A.S. / Gilman, A.G. / Sprang, S.R.
#1: Journal: Science / Year: 1995
Title: Tertiary and Quaternary Structural Changes in Gi Alpha 1 Induced by GTP Hydrolysis
Authors: Mixon, M.B. / Lee, E. / Coleman, D.E. / Berghuis, A.M. / Gilman, A.G. / Sprang, S.R.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Studies of Gi Alpha 1 and Mutants of Gi Alpha 1 in the GTP and Gdp-Bound States
Authors: Coleman, D.E. / Lee, E. / Mixon, M.B. / Linder, M.E. / Berghuis, A.M. / Gilman, A.G. / Sprang, S.R.
#3: Journal: Science / Year: 1994
Title: Structures of Active Conformations of Gi Alpha 1 and the Mechanism of GTP Hydrolysis
Authors: Coleman, D.E. / Berghuis, A.M. / Lee, E. / Linder, M.E. / Gilman, A.G. / Sprang, S.R.
History
DepositionOct 16, 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G PROTEIN GI ALPHA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8203
Polymers40,2821
Non-polymers5382
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.100, 77.100, 144.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein G PROTEIN GI ALPHA 1


Mass: 40281.863 Da / Num. of mol.: 1 / Fragment: ALPHA 1 / Mutation: G203A
Source method: isolated from a genetically manipulated source
Details: STRUCTURE MIMICS THE TERNARY COMPLEX / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PQE6 VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P10824
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.67 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
22.5 mM1dropMgSO4
30.25 mMEDTA1drop
42.5 mMdithiothreitol1drop
52.5 mMGTPgammaS1drop
612.5 mMNaEPPS1drop
71.1-1.25 Mammonium sulfate1drop
82.2-2.5 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979
DetectorType: FUJI / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionNum. obs: 11856 / % possible obs: 84.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. measured all: 28864 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 86.5 % / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.6→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1137 10.4 %RANDOM
Rwork0.186 ---
obs0.186 10917 81 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 33 9 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.51.5
X-RAY DIFFRACTIONx_mcangle_it5.522
X-RAY DIFFRACTIONx_scbond_it5.322
X-RAY DIFFRACTIONx_scangle_it7.592.5
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.336 126 9.9 %
Rwork0.231 1149 -
obs--77.6 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51
LS refinement shell
*PLUS
Rfactor obs: 0.231

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