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- PDB-4pan: A conserved phenylalanine as relay between the 5 helix and the GD... -

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Basic information

Entry
Database: PDB / ID: 4pan
TitleA conserved phenylalanine as relay between the 5 helix and the GDP binding region of heterotrimeric G protein
ComponentsGuanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsSIGNALING PROTEIN / Activation of Heterotrimeric G protein / GDP release / Computer modeling / G protein Coupled Receptors / Rhodopsin
Function / homology
Function and homology information


Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / 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 ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / 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 / SULFITE ION / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKaya, A.I. / Lokits, A.D. / Gilbert, J. / Iverson, T.M. / Meiler, J. / Hamm, H.E.
Funding support United States, 10items
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 GM095633 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM080403 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1 MH090192 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1 MH090192 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM099842 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1 DK09737 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
National Science Foundation (NSF, United States)0742762 United States
National Science Foundation (NSF, United States)1305874 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Conserved Phenylalanine as a Relay between the alpha 5 Helix and the GDP Binding Region of Heterotrimeric Gi Protein alpha Subunit.
Authors: Kaya, A.I. / Lokits, A.D. / Gilbert, J.A. / Iverson, T.M. / Meiler, J. / Hamm, H.E.
History
DepositionApr 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Refinement description
Category: database_2 / pdbx_audit_support / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9744
Polymers40,4151
Non-polymers5593
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-19 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.533, 121.533, 68.279
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) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40415.031 Da / Num. of mol.: 1 / Mutation: F336Y
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: 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-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO3, Sodium acetate / PH range: 5.9-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19424 / % possible obs: 99.2 % / Redundancy: 4.3 % / Net I/σ(I): 19.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.4→20 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1930 9.94 %
Rwork0.1822 --
obs0.1872 19424 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 33 88 2706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082659
X-RAY DIFFRACTIONf_angle_d1.0113583
X-RAY DIFFRACTIONf_dihedral_angle_d14.279989
X-RAY DIFFRACTIONf_chiral_restr0.071400
X-RAY DIFFRACTIONf_plane_restr0.004453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.460.29211380.22481201X-RAY DIFFRACTION99
2.46-2.52640.26171330.21371282X-RAY DIFFRACTION100
2.5264-2.60050.27041280.20321255X-RAY DIFFRACTION100
2.6005-2.68430.32111360.2061253X-RAY DIFFRACTION100
2.6843-2.780.28231510.20671225X-RAY DIFFRACTION100
2.78-2.8910.281490.20111262X-RAY DIFFRACTION100
2.891-3.02210.24151570.20441212X-RAY DIFFRACTION100
3.0221-3.18080.27021330.21541287X-RAY DIFFRACTION100
3.1808-3.37920.28831550.20691203X-RAY DIFFRACTION100
3.3792-3.63860.23791330.18751249X-RAY DIFFRACTION99
3.6386-4.00210.22891180.17231240X-RAY DIFFRACTION96
4.0021-4.5750.18231420.15051245X-RAY DIFFRACTION100
4.575-5.74080.20271170.15521303X-RAY DIFFRACTION99
5.7408-19.84320.17651400.16621277X-RAY DIFFRACTION99

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