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- PDB-5js7: Structural model of a apo G-protein alpha subunit determined with... -

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Basic information

Entry
Database: PDB / ID: 5js7
TitleStructural model of a apo G-protein alpha subunit determined with NMR residual dipolar couplings and SAXS
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / G-proteins / NMR. SAXS / GPCR
Function / homology
Function and homology information


Adenylate cyclase inhibitory pathway / 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 / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding ...Adenylate cyclase inhibitory pathway / 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 / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / 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
Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGoricanec, D. / Stehle, R. / Grigoriu, S. / Wagner, G. / Hagn, F.
Funding support United States, Germany, France, 7items
OrganizationGrant numberCountry
National Institutes of HealthGM075879 United States
National Institutes of HealthGM047467 United States
National Institutes of HealthGM094608 United States
National Institutes of HealthEB002026 United States
European Commission291763 Germany
Center for Integrated Protein Science Munich Germany
HFSPLT-000297/2011 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Conformational dynamics of a G-protein alpha subunit is tightly regulated by nucleotide binding.
Authors: Goricanec, D. / Stehle, R. / Egloff, P. / Grigoriu, S. / Pluckthun, A. / Wagner, G. / Hagn, F.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.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) subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)37,2471
Polymers37,2471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16160 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 37247.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P63096

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCO
121isotropic23D HNCA
131isotropic23D HN(CO)CA
151isotropic23D HN(CA)CB
162isotropic32D 1H-15N HSQC
272anisotropic32D 1H-15N HSQC
181isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1400 uM [U-98% 2H; U-99% 13C; U-99% 15N] G protein alpha subunit subtype i1, GNAI1, 95% H2O/5% D2OGNAI1_DCN95% H2O/5% D2O
solution2250 uM [U-98% 15N; U-90% 2H] G protein alpha subunit subtype i1, GNAI1, 95% H2O/5% D2OGNAI1_DN95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMG protein alpha subunit subtype i1, GNAI1[U-98% 2H; U-99% 13C; U-99% 15N]1
250 uMG protein alpha subunit subtype i1, GNAI1[U-98% 15N; U-90% 2H]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
1100 mMstandard7.0 1 atm303 K
2100 mManisotropic7.0 1 atm303 Kstandard conditions + 8mg / mL Pf1 phage

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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