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- PDB-5js8: Structural Model of a Protein alpha subunit in complex with GDP o... -

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Basic information

Entry
Database: PDB / ID: 5js8
TitleStructural Model of a Protein alpha subunit in complex with GDP obtained with SAXS and NMR residual couplings
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / G-proteins / SAXS / singling / 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 / cellular response to forskolin / regulation of mitotic spindle organization / 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 / cellular response to forskolin / regulation of mitotic spindle organization / 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 / G protein-coupled receptor signaling pathway / cell cycle / lysosomal membrane / cell division / GTPase activity / centrosome / nucleolus / GTP binding / 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 Germany, France, United States, 7items
OrganizationGrant numberCountry
Center for Integrated Protein Science Germany
European Union291763 Germany
Human Frontier Science ProgramLT00029712011-L France
National Institutes of HealthGM075879 United States
National Institutes of HealthGM047467 United States
National Institutes of HealthGM094608 United States
National Institutes of HealthEB002026 United States
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 area16120 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 / Details (production host): pQE30-GB1-TEV / Production host: Escherichia coli (E. coli) / 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
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HN(CO)CA
151isotropic13D 1H-15N NOESY
171isotropic12D 1H-15N HSQC
162isotropic22D 1H-15N HSQC
282anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1400 uM [U-95% 2H; U-98% 13C; U-98% 15N] G protein alpha subunit, subtype i,1, 95% H2O/5% D2OGNAI1_GDP_DCN95% H2O/5% D2O
solution2250 uM [U-90% 2H; U-98% 15N] G protein alpha subunit, subtype i,1, 95% H2O/5% D2OGNAI1_GDP-DN95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMG protein alpha subunit, subtype i,1[U-95% 2H; U-98% 13C; U-98% 15N]1
250 uMG protein alpha subunit, subtype i,1[U-90% 2H; U-98% 15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1+ 5mM GDP + 5mM MgCl2100 mMstandard7.0 1 atm303 K
2+ 5 mM GDP + 5 mM MgCl2 + 8 mg/mL Pf1 phage100 mManisotropic7.0 1 atm303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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