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- PDB-5kdo: Heterotrimeric complex of the 4 alanine insertion variant of the ... -

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Basic information

Entry
Database: PDB / ID: 5kdo
TitleHeterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and the Gbeta1-Ggamma1
Components
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Guanine nucleotide-binding protein G(T) subunit gamma-T1
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / Heterotrimeric G protein G protein Coupled Receptors G protein activation G protein structure GDP release
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) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / negative regulation of synaptic transmission / GTPase activating protein binding ...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) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / 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 / G alpha (q) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / phototransduction / 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 / 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 / retina development in camera-type eye / G protein activity / GTPase binding / midbody / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / P-loop containing nucleotide triphosphate hydrolases / Trp-Asp (WD) repeats signature. / 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(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKaya, A.I. / Lokits, A.D. / Gilbert, J. / Iverson, T.M. / Meiler, J. / Hamm, H.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)RO1 EY006062 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM120569 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM080403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Conserved Hydrophobic Core in G alpha i1 Regulates G Protein Activation and Release from Activated Receptor.
Authors: Kaya, A.I. / Lokits, A.D. / Gilbert, J.A. / Iverson, T.M. / Meiler, J. / Hamm, H.E.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(T) subunit gamma-T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1004
Polymers86,6573
Non-polymers4431
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-55 kcal/mol
Surface area32790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.648, 84.648, 130.091
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 Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40683.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai1, Gnai-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNB1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Transducin gamma chain


Mass: 8556.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNGT1 / Production host: Bos taurus (domestic cattle) / 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.: 305 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 19-24 % PEG 8000, 1-5% 2-propanolol, 1% OG, 100 mM HEPES (pH 7.0) and 100 mM NaOAc (pH 6.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→40.248 Å / Num. obs: 71880 / % possible obs: 100 % / Redundancy: 8.5 % / Rsym value: 0.074 / Net I/σ(I): 17.44
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.36 / Rsym value: 1.234 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP2

1gp2


Resolution: 1.9→40.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.208 7202 10.02 %
Rwork0.182 --
obs0.185 71880 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 28 305 6083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075881
X-RAY DIFFRACTIONf_angle_d0.9777942
X-RAY DIFFRACTIONf_dihedral_angle_d19.4842165
X-RAY DIFFRACTIONf_chiral_restr0.079884
X-RAY DIFFRACTIONf_plane_restr0.0051023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92170.30342240.29212166X-RAY DIFFRACTION100
1.9217-1.94430.3042720.27412098X-RAY DIFFRACTION100
1.9443-1.9680.29642680.26352146X-RAY DIFFRACTION100
1.968-1.9930.23712530.23762100X-RAY DIFFRACTION100
1.993-2.01920.26742470.23112142X-RAY DIFFRACTION100
2.0192-2.04680.25912760.22852094X-RAY DIFFRACTION100
2.0468-2.07610.24612660.22152156X-RAY DIFFRACTION100
2.0761-2.10710.24642330.21262170X-RAY DIFFRACTION100
2.1071-2.140.24692120.22052164X-RAY DIFFRACTION100
2.14-2.17510.25842070.22112183X-RAY DIFFRACTION100
2.1751-2.21260.23742580.20332144X-RAY DIFFRACTION100
2.2126-2.25280.22682000.20022186X-RAY DIFFRACTION100
2.2528-2.29610.22072240.19372177X-RAY DIFFRACTION100
2.2961-2.3430.21382240.18862172X-RAY DIFFRACTION100
2.343-2.39390.21342330.19522155X-RAY DIFFRACTION100
2.3939-2.44960.23512440.19322130X-RAY DIFFRACTION100
2.4496-2.51090.21012240.18622168X-RAY DIFFRACTION100
2.5109-2.57870.2222590.18342137X-RAY DIFFRACTION100
2.5787-2.65460.23552340.18912181X-RAY DIFFRACTION100
2.6546-2.74030.23062750.18792104X-RAY DIFFRACTION100
2.7403-2.83820.19472440.18042163X-RAY DIFFRACTION100
2.8382-2.95180.2442200.18632162X-RAY DIFFRACTION100
2.9518-3.08610.20592360.1892150X-RAY DIFFRACTION100
3.0861-3.24870.19822460.18352182X-RAY DIFFRACTION100
3.2487-3.45220.22151960.18962196X-RAY DIFFRACTION100
3.4522-3.71850.2252450.17432167X-RAY DIFFRACTION100
3.7185-4.09240.15362310.14912171X-RAY DIFFRACTION100
4.0924-4.68380.16022460.13362166X-RAY DIFFRACTION100
4.6838-5.89820.17332630.14412149X-RAY DIFFRACTION100
5.8982-40.25650.17832420.17732199X-RAY DIFFRACTION99

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