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- PDB-2ihb: Crystal structure of the heterodimeric complex of human RGS10 and... -

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Basic information

Entry
Database: PDB / ID: 2ihb
TitleCrystal structure of the heterodimeric complex of human RGS10 and activated Gi alpha 3
Components
  • Guanine nucleotide-binding protein G(k) subunit alpha
  • Regulator of G-protein signalling 10
KeywordsSIGNALING PROTEIN / G protein signalling / RGS / heterotrimeric G protein / signalling complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / GTP metabolic process / positive regulation of macroautophagy / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / Adenylate cyclase inhibitory pathway / GTPase activator activity / G protein-coupled receptor binding ...negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / GTP metabolic process / positive regulation of macroautophagy / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / Adenylate cyclase inhibitory pathway / GTPase activator activity / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / centriolar satellite / G protein-coupled acetylcholine receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / GDP binding / G alpha (z) signalling events / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / heterotrimeric G-protein complex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / Extra-nuclear estrogen signaling / nuclear body / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / synapse / centrosome / GTP binding / nucleolus / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RGS10, RGS domain / : / 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 ...RGS10, RGS domain / : / 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 domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 10 / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Regulator of G-protein signaling 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSoundararajan, M. / Turnbull, A.P. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Ugochukwu, E. / Gorrec, F. / von Delft, F. / Weigelt, J. / Edwards, A. ...Soundararajan, M. / Turnbull, A.P. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Ugochukwu, E. / Gorrec, F. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural diversity in the RGS domain and its interaction with heterotrimeric G protein alpha-subunits.
Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / Doyle, D.A. / Siderovski, D.P.
History
DepositionSep 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_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_ref_seq_dif.details / _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 signalling 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7935
Polymers55,2232
Non-polymers5703
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.628, 100.628, 145.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / Gi / alpha-3


Mass: 37201.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P08754
#2: Protein Regulator of G-protein signalling 10


Mass: 18021.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS10 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: Q96GN0, UniProt: O43665*PLUS

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Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M (NH4)2SO4, 0.1M Bis-Tris, pH 5.5, 25% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97925 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 20815 / Num. obs: 20470 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.75 Å / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based on the coordinates of PDB entries 1agr, 1ezt, 1ezy, 2bv1

1agr

1ezt

1ezy

2bv1


Resolution: 2.71→47.6 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.321 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23632 1040 5.1 %RANDOM
Rwork0.20763 ---
all0.20913 19430 --
obs0.20913 19430 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.111 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--2.07 Å20 Å2
3----4.13 Å2
Refinement stepCycle: LAST / Resolution: 2.71→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 34 18 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223497
X-RAY DIFFRACTIONr_bond_other_d0.0010.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9574725
X-RAY DIFFRACTIONr_angle_other_deg0.80635697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46924.485165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24815612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7651518
X-RAY DIFFRACTIONr_chiral_restr0.0550.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
X-RAY DIFFRACTIONr_nbd_refined0.2130.2763
X-RAY DIFFRACTIONr_nbd_other0.1730.22332
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21722
X-RAY DIFFRACTIONr_nbtor_other0.0830.21840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0560.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0270.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.52186
X-RAY DIFFRACTIONr_mcbond_other0.0531.5865
X-RAY DIFFRACTIONr_mcangle_it0.70223420
X-RAY DIFFRACTIONr_scbond_it0.89531507
X-RAY DIFFRACTIONr_scangle_it1.474.51305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.71→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 57 -
Rwork0.322 1144 -
obs--80.23 %
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)
13.46710.43011.0511.97550.55563.1447-0.03920.0019-0.0201-0.0515-0.05070.21770.0105-0.10760.0899-0.1741-0.02660.0169-0.1096-0.0021-0.2642-6.4394-25.4049-31.3374
25.77230.4006-1.44855.8487-0.87346.4491-0.0457-0.38310.0060.43230.01210.1024-0.20320.13670.0335-0.1290.05030.0443-0.0353-0.084-0.2083-6.3296-16.4536-7.1103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 3482 - 317
2X-RAY DIFFRACTION2BB24 - 10225 - 103
3X-RAY DIFFRACTION2BB114 - 145115 - 146

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