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- PDB-2ode: Crystal structure of the heterodimeric complex of human RGS8 and ... -

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Basic information

Entry
Database: PDB / ID: 2ode
TitleCrystal structure of the heterodimeric complex of human RGS8 and activated Gi alpha 3
Components
  • Guanine nucleotide-binding protein G(k) subunit alpha
  • Regulator of G-protein signaling 8
KeywordsSIGNALING PROTEIN / G protein signalling / RGS / heterotrimeric G protein / signalling complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of dopamine receptor signaling pathway / negative regulation of adenylate cyclase activity / GTP metabolic process / neuronal cell body membrane / positive regulation of macroautophagy / positive regulation of GTPase activity / negative regulation of signal transduction / Adenylate cyclase inhibitory pathway / GTPase activator activity / G protein-coupled receptor binding ...regulation of dopamine receptor signaling pathway / negative regulation of adenylate cyclase activity / GTP metabolic process / neuronal cell body membrane / positive regulation of macroautophagy / positive regulation of GTPase activity / 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 / cytoplasmic side of plasma membrane / centriolar satellite / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / 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 / perikaryon / Extra-nuclear estrogen signaling / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / synapse / dendrite / centrosome / GTP binding / nucleolus / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 8, 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 ...Regulator of G-protein signalling 8, 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 / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Regulator of G-protein signaling 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGileadi, C. / Soundararajan, M. / Turnbull, A.P. / Elkins, J.M. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Gorrec, F. / Umeano, C. / von Delft, F. ...Gileadi, C. / Soundararajan, M. / Turnbull, A.P. / Elkins, J.M. / Papagrigoriou, E. / Pike, A.C.W. / Bunkoczi, G. / Gorrec, F. / Umeano, C. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / 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
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: 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_ncs_dom_lim / 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_asym_id / _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_asym_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_asym_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_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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 signaling 8
C: Guanine nucleotide-binding protein G(k) subunit alpha
D: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,70410
Polymers113,5634
Non-polymers1,1416
Water11,800655
1
A: Guanine nucleotide-binding protein G(k) subunit alpha
B: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3525
Polymers56,7812
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Guanine nucleotide-binding protein G(k) subunit alpha
D: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3525
Polymers56,7812
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.837, 130.216, 68.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA33 - 34832 - 347
21GLUGLUASNASNCC33 - 34732 - 346
12SERSERGLNGLNBB46 - 1767 - 137
22SERSERLEULEUDD56 - 17117 - 132

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Guanine nucleotide-binding protein G(k) subunit alpha / Gi / alpha-3


Mass: 40162.578 Da / Num. of mol.: 2
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 signaling 8 / RGS8


Mass: 16618.889 Da / Num. of mol.: 2 / Fragment: residues 42-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS8 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 / References: UniProt: P57771

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Non-polymers , 4 types, 661 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M NH4Cl, 20.0% PEG 6K, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 80222 / Num. obs: 80222 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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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: PDB ENTRY 2IHB

2ihb


Resolution: 1.9→29.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.958 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21105 4021 5 %RANDOM
Rwork0.17988 ---
all0.18148 76139 --
obs0.18148 76139 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2---1.36 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6980 0 68 655 7703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227238
X-RAY DIFFRACTIONr_bond_other_d0.0020.024842
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9559807
X-RAY DIFFRACTIONr_angle_other_deg0.953311783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16124.265347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.153151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8831542
X-RAY DIFFRACTIONr_chiral_restr0.0810.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021545
X-RAY DIFFRACTIONr_nbd_refined0.2150.21505
X-RAY DIFFRACTIONr_nbd_other0.1910.25049
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23554
X-RAY DIFFRACTIONr_nbtor_other0.0860.23482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7861.54556
X-RAY DIFFRACTIONr_mcbond_other0.2231.51788
X-RAY DIFFRACTIONr_mcangle_it1.15927098
X-RAY DIFFRACTIONr_scbond_it1.90533100
X-RAY DIFFRACTIONr_scangle_it2.824.52699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1863medium positional0.130.5
2B688medium positional0.120.5
1A2214loose positional0.435
2B868loose positional0.565
1A1863medium thermal0.722
2B688medium thermal0.922
1A2214loose thermal1.2210
2B868loose thermal1.1510
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 295 -
Rwork0.261 5455 -
obs--97.71 %
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)
11.4930.09910.23411.99590.29051.8415-0.04330.0362-0.19820.01590.0344-0.13760.16760.01320.0089-0.1468-0.0063-0.0031-0.2156-0.0313-0.118919.61598.592530.4741
24.6891-1.16271.12012.1562-0.32482.3851-0.2213-0.31130.46490.22050.1004-0.3472-0.30040.06190.1208-0.0764-0.0367-0.0549-0.1884-0.0502-0.113224.989431.748338.6334
31.7320.0428-0.42472.4960.28311.98770.00360.2157-0.0295-0.1359-0.0331-0.162-0.2488-0.19010.0294-0.12180.00170.0124-0.1647-0.0035-0.165312.34950.14316.4319
42.42440.9522-0.39613.0537-0.40974.2115-0.02450.1762-0.2131-0.24460.151-0.12510.3109-0.2462-0.1265-0.1495-0.0574-0.0078-0.1175-0.0453-0.14063.002726.97462.8948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 34832 - 347
2X-RAY DIFFRACTION2BB46 - 1767 - 137
3X-RAY DIFFRACTION3CC31 - 34730 - 346
4X-RAY DIFFRACTION4DD56 - 17117 - 132

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