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- PDB-5kdl: Crystal structure of the 4 alanine insertion variant of the Gi al... -

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Basic information

Entry
Database: PDB / ID: 5kdl
TitleCrystal structure of the 4 alanine insertion variant of the Gi alpha1 subunit bound to GTPgammaS
ComponentsGuanine 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 / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / GTPase activating protein binding / negative regulation of synaptic transmission / G alpha (i) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / D2 dopamine receptor binding / positive regulation of protein localization to cell cortex ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / GTPase activating protein binding / negative regulation of synaptic transmission / G alpha (i) signalling events / neurotransmitter receptor localization to postsynaptic specialization membrane / D2 dopamine receptor binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / glutamatergic synapse / 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 / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.665 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)RO1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4946
Polymers81,3672
Non-polymers1,1274
Water724
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2473
Polymers40,6831
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanine nucleotide-binding protein G(i) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2473
Polymers40,6831
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.742, 77.351, 73.095
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 12-16 % polyethylene glycol (PEG) 2000 monomethyl ether, 18% 2-propanol and 100 mM MES (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.66→47.816 Å / Num. obs: 19135 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.088 / Net I/σ(I): 14.4
Reflection shellResolution: 2.66→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.04 / Rsym value: 0.571 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GIA

1gia


Resolution: 2.665→47.816 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1871 9.84 %
Rwork0.2093 --
obs0.2148 19008 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.665→47.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 66 4 5030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035116
X-RAY DIFFRACTIONf_angle_d0.5416911
X-RAY DIFFRACTIONf_dihedral_angle_d15.8633075
X-RAY DIFFRACTIONf_chiral_restr0.038770
X-RAY DIFFRACTIONf_plane_restr0.002869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6649-2.73690.33991010.3059934X-RAY DIFFRACTION70
2.7369-2.81750.36011360.26291363X-RAY DIFFRACTION99
2.8175-2.90840.32191570.26411320X-RAY DIFFRACTION100
2.9084-3.01230.31471480.24141331X-RAY DIFFRACTION100
3.0123-3.13290.32051510.24821345X-RAY DIFFRACTION100
3.1329-3.27550.30271300.24251348X-RAY DIFFRACTION100
3.2755-3.44810.31621520.21821359X-RAY DIFFRACTION100
3.4481-3.66410.30521500.20511358X-RAY DIFFRACTION100
3.6641-3.94680.24821250.19651353X-RAY DIFFRACTION100
3.9468-4.34380.22211410.18221353X-RAY DIFFRACTION100
4.3438-4.97180.2231490.18531359X-RAY DIFFRACTION100
4.9718-6.26170.251640.21251344X-RAY DIFFRACTION100
6.2617-47.82350.23441670.19171370X-RAY DIFFRACTION99

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