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- PDB-2v4z: The crystal structure of the human G-protein subunit alpha (GNAI3... -

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Basic information

Entry
Database: PDB / ID: 2v4z
TitleThe crystal structure of the human G-protein subunit alpha (GNAI3) in complex with an engineered regulator of G-protein signaling type 2 domain (RGS2)
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(K) SUBUNIT ALPHA
  • REGULATOR OF G-PROTEIN SIGNALING 2
KeywordsCELL CYCLE / GTP HYDROLYSIS / ADP-RIBOSYLATION / NUCLEOTIDE-BINDING / LIPOPROTEIN / GTP-BINDING / PHOSPHOPROTEIN / SIGNAL TRANSDUCTION INHIBITOR / GUANINE NUCLEOTIDE BINDING PROTEIN / TRANSMEMBRANE SIGNALING / G-PROTEIN COUPLED RECEPTOR / PALMITATE / MYRISTATE / TRANSDUCER
Function / homology
Function and homology information


regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / adenylate cyclase inhibitor activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / relaxation of vascular associated smooth muscle ...regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / adenylate cyclase inhibitor activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cell growth involved in cardiac muscle cell development / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / relaxation of vascular associated smooth muscle / GTP metabolic process / relaxation of cardiac muscle / dopamine receptor signaling pathway / beta-tubulin binding / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / G-protein alpha-subunit binding / maternal process involved in female pregnancy / brown fat cell differentiation / positive regulation of cardiac muscle contraction / response to amphetamine / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / negative regulation of MAP kinase activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / positive regulation of neuron projection development / ADP signalling through P2Y purinoceptor 12 / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / spermatogenesis / response to ethanol / negative regulation of translation / Extra-nuclear estrogen signaling / calmodulin binding / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / mitochondrion / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 2 / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 ...Regulator of G-protein signalling 2 / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / RGS, subdomain 1/3 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Regulator of G-protein signaling 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRoos, A.K. / Soundararajan, M. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Determinants of G-Protein Alpha Subunit Selectivity by Regulator of G-Protein Signaling 2(Rgs2).
Authors: Kimple, A.J. / Soundararajan, M. / Hutsell, S.Q. / Roos, A.K. / Urban, D.J. / Setola, V. / Temple, B.R. / Roth, B.L. / Knapp, S. / Willard, F.S. / Siderovski, D.P.
History
DepositionSep 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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(K) SUBUNIT ALPHA
B: REGULATOR OF G-PROTEIN SIGNALING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1945
Polymers56,6232
Non-polymers5703
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8.2 kcal/mol
Surface area24060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)114.539, 114.539, 99.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(K) SUBUNIT ALPHA / G(I) ALPHA-3 / GUANINE NUCLEOTIDE-BINDING PROTEIN G K SUBUNIT ALPHA G I ALPHA-3


Mass: 40162.578 Da / Num. of mol.: 1 / Fragment: SUBUNIT ALPHA, RESIDUES 4-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P08754
#2: Protein REGULATOR OF G-PROTEIN SIGNALING 2 / G0/G1 SWITCH REGULATORY PROTEIN 8 / RGS2 / CELL GROWTH-INHIBITING GENE 31 PROTEIN


Mass: 16460.529 Da / Num. of mol.: 1 / Fragment: RGS DOMAIN, RESIDUES 71-209 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P41220

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Non-polymers , 4 types, 21 molecules

#3: 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
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, CYS 106 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 184 TO ASP ...ENGINEERED RESIDUE IN CHAIN B, CYS 106 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 184 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 191 TO LYS
Sequence detailsTRIPLE MUTANT C106S, N184D, E191K

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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: 3.47 Å3/Da / Density % sol: 64.6 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 2, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→35.09 Å / Num. obs: 18916 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 7.2 % / Biso Wilson estimate: 67.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IHB

2ihb


Resolution: 2.8→33.37 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 27.265 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 959 5.1 %RANDOM
Rwork0.208 ---
obs0.21 17941 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 34 18 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223495
X-RAY DIFFRACTIONr_bond_other_d0.0010.022285
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9544740
X-RAY DIFFRACTIONr_angle_other_deg0.78635553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15824.417163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46415561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7371518
X-RAY DIFFRACTIONr_chiral_restr0.0510.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2681.52177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52123478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7431318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2884.51262
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 60
Rwork0.329 1307
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.31470.4059-0.74452.5912-0.02233.0780.0873-0.1791-0.2075-0.0661-0.1899-0.2548-0.05860.20740.1026-0.3001-0.0007-0.0515-0.22770.032-0.3305-0.762445.7584-9.8955
24.8342-1.4769-2.20165.2818-1.9847.4831-0.1026-0.8716-0.31951.68980.16820.70530.16430.1155-0.06550.23550.0580.0820.23660.25390.0106-5.839336.129711.9945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 347
2X-RAY DIFFRACTION1A1348
3X-RAY DIFFRACTION1A1349
4X-RAY DIFFRACTION2B72 - 199

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