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- PDB-3ffb: Gi-alpha-1 mutant in GDP bound form -

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Basic information

Entry
Database: PDB / ID: 3ffb
TitleGi-alpha-1 mutant in GDP bound form
ComponentsGuanine nucleotide-binding protein G(i), alpha-1 subunit
KeywordsSIGNALING PROTEIN / Gi-alpha-1 fast activating mutant / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Transducer / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / cell cortex region / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / cell cortex region / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsChauhan, R. / Kapoor, N.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural evidence for a sequential release mechanism for activation of heterotrimeric g proteins.
Authors: Kapoor, N. / Menon, S.T. / Chauhan, R. / Sachdev, P. / Sakmar, T.P.
History
DepositionDec 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i), alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4903
Polymers40,9511
Non-polymers5392
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.761, 121.761, 68.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Guanine nucleotide-binding protein G(i), alpha-1 subunit / Adenylate cyclase-inhibiting G alpha protein


Mass: 40950.672 Da / Num. of mol.: 1 / Mutation: T329A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gi-alpha-1, Gnai-1, Gnai1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10824
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 100 mM Sodium Acetate pH 5.9-6.3, 1.8-2.1 M Ammonium Sulphate, VAPOR DIFFUSION, temperature 293K, pH 6.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.57→59.8 Å / Num. obs: 16157 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 58.45 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.57→2.7 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 7.4 / Num. unique all: 17350 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOF

1bof


Resolution: 2.57→59.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.319 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 810 5 %RANDOM
Rwork0.181 ---
obs-15347 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.57→59.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 33 46 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222676
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9683604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18624.531128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1261516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021972
X-RAY DIFFRACTIONr_nbd_refined0.2030.21171
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.210
X-RAY DIFFRACTIONr_mcbond_it1.1161.51664
X-RAY DIFFRACTIONr_mcangle_it1.9522593
X-RAY DIFFRACTIONr_scbond_it2.61431155
X-RAY DIFFRACTIONr_scangle_it4.14.51011
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 48 -
Rwork0.226 1144 -
obs--100 %

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