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- PDB-5do9: Structure of regulator of G protein signaling 8 (RGS8) in complex... -

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Basic information

Entry
Database: PDB / ID: 5do9
TitleStructure of regulator of G protein signaling 8 (RGS8) in complex with AlF4-activated Galpha-q
Components
  • Guanine nucleotide-binding protein G(q) subunit alpha
  • Regulator of G-protein signaling 8
KeywordsPROTEIN BINDING / GTP-Binding Protein alpha subunits / Gq-G11 / RGS proteins
Function / homology
Function and homology information


Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / G alpha (q) signalling events ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / G alpha (q) signalling events / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / phospholipase C-activating dopamine receptor signaling pathway / regulation of dopamine receptor signaling pathway / cranial skeletal system development / regulation of platelet activation / ADP signalling through P2Y purinoceptor 1 / maternal behavior / glutamate receptor signaling pathway / regulation of canonical Wnt signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / action potential / neuronal cell body membrane / neuron remodeling / embryonic digit morphogenesis / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / enzyme regulator activity / negative regulation of signal transduction / GTPase activator activity / post-embryonic development / G protein activity / skeletal system development / G protein-coupled receptor binding / caveola / positive regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / G protein-coupled acetylcholine receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / positive regulation of insulin secretion / positive regulation of GTPase activity / regulation of blood pressure / heterotrimeric G-protein complex / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (i) signalling events / perikaryon / nuclear membrane / protein stabilization / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / protein-containing complex binding / GTP binding / negative regulation of apoptotic process / Golgi apparatus / membrane / metal ion binding / nucleus / plasma membrane
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 / G-protein alpha subunit, group Q / 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 ...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 / G-protein alpha subunit, group Q / 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-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(q) subunit alpha / Regulator of G-protein signaling 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsTaylor, V.G. / Tesmer, J.J.G.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of the Regulator of G Protein Signaling 8 (RGS8)-G alpha q Complex: MOLECULAR BASIS FOR G alpha SELECTIVITY.
Authors: Taylor, V.G. / Bommarito, P.A. / Tesmer, J.J.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5Mar 6, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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(q) subunit alpha
B: Regulator of G-protein signaling 8
C: Guanine nucleotide-binding protein G(q) subunit alpha
D: Regulator of G-protein signaling 8
E: Guanine nucleotide-binding protein G(q) subunit alpha
F: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,55615
Polymers157,8446
Non-polymers1,7119
Water4,161231
1
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Guanine nucleotide-binding protein G(q) subunit alpha
D: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Guanine nucleotide-binding protein G(q) subunit alpha
F: Regulator of G-protein signaling 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Guanine nucleotide-binding protein G(q) subunit alpha
hetero molecules

D: Regulator of G-protein signaling 8


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2870 Å2
ΔGint-25 kcal/mol
Surface area21770 Å2
MethodPISA
5
C: Guanine nucleotide-binding protein G(q) subunit alpha
hetero molecules

B: Regulator of G-protein signaling 8


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2890 Å2
ΔGint-23 kcal/mol
Surface area21730 Å2
MethodPISA
6
E: Guanine nucleotide-binding protein G(q) subunit alpha
hetero molecules

F: Regulator of G-protein signaling 8


Theoretical massNumber of molelcules
Total (without water)53,1855
Polymers52,6152
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area2840 Å2
ΔGint-26 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.946, 95.881, 112.898
Angle α, β, γ (deg.)90.000, 94.310, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLNGLNAA37 - 3501 - 314
21ARGARGGLNGLNCC37 - 3501 - 314
12ARGARGLEULEUAA38 - 3492 - 313
22ARGARGLEULEUEE38 - 3492 - 313
13SERSERSERSERBB40 - 1731 - 134
23SERSERSERSERDD40 - 1731 - 134
14SERSERSERSERBB40 - 1731 - 134
24SERSERSERSERFF40 - 1731 - 134
15ARGARGLEULEUCC38 - 3492 - 313
25ARGARGLEULEUEE38 - 3492 - 313
16SERSERSERSERDD40 - 1731 - 134
26SERSERSERSERFF40 - 1731 - 134

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein alpha-q


Mass: 36853.871 Da / Num. of mol.: 3
Fragment: Guanine nucleotide-binding protein G(q) subunit alpha
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Plasmid: pFastbac HT A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21279
#2: Protein Regulator of G-protein signaling 8 / RGS8


Mass: 15760.928 Da / Num. of mol.: 3 / Fragment: RGS Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS8 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P57771

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Non-polymers , 4 types, 240 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Ammonium acetate, BisTris pH 5.5, PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0383 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0383 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 56869 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.075 / Rrim(I) all: 0.146 / Χ2: 1.764 / Net I/av σ(I): 14.233 / Net I/σ(I): 7.6 / Num. measured all: 211145
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.60.58527500.7150.3580.6870.66797.6
2.64-2.693.80.52928290.7690.3130.6160.701100
2.69-2.743.80.47928620.7920.2830.5560.717100
2.74-2.83.80.40728070.8480.2410.4730.763100
2.8-2.863.80.35528330.8890.210.4130.823100
2.86-2.933.80.30628470.8920.1810.3560.897100
2.93-33.80.28628520.9120.170.3330.997100
3-3.083.80.2428260.9270.1420.2791.119100
3.08-3.173.80.21428230.9430.1270.2491.293100
3.17-3.283.80.18228400.9570.1080.2111.482100
3.28-3.393.80.15928330.9690.0940.1851.713100
3.39-3.533.80.14128580.9760.0840.1651.992100
3.53-3.693.70.12528540.9810.0750.1462.31699.9
3.69-3.883.70.10828240.9860.0650.1262.526100
3.88-4.123.60.09328520.9890.0560.1092.85199.9
4.12-4.443.60.08228380.990.050.0963.07499.8
4.44-4.893.50.07328620.9920.0450.0863.11699.9
4.89-5.593.60.07828710.9910.0470.0913.0899.9
5.59-7.033.60.0828930.990.0490.0932.947100
7.03-303.40.04829150.9960.030.0562.78399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.8 Å29.55 Å
Translation7.8 Å29.55 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1592 / FOM work R set: 0.827 / SU B: 23.884 / SU ML: 0.219 / SU R Cruickshank DPI: 0.5517 / SU Rfree: 0.2745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.552 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 2833 5 %RANDOM
Rwork0.178 ---
obs0.1804 54036 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 256.16 Å2 / Biso mean: 47.491 Å2 / Biso min: 18.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.44 Å2
2---1.67 Å20 Å2
3---1.96 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11092 0 102 231 11425
Biso mean--27.12 37.71 -
Num. residues----1343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911431
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210769
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.96415439
X-RAY DIFFRACTIONr_angle_other_deg1.505324767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60651337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0223.697587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86152073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1491592
X-RAY DIFFRACTIONr_chiral_restr0.0880.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212717
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022749
X-RAY DIFFRACTIONr_mcbond_it1.5822.0135366
X-RAY DIFFRACTIONr_mcbond_other1.5812.0125365
X-RAY DIFFRACTIONr_mcangle_it2.6233.016697
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A191780.14
12C191780.14
21A193090.13
22E193090.13
31B77730.14
32D77730.14
41B76290.15
42F76290.15
51C189990.15
52E189990.15
61D76120.16
62F76120.16
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 183 -
Rwork0.27 3705 -
all-3888 -
obs--92.33 %
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)
11.31570.3186-0.00251.21960.34451.7411-0.05320.14840.0653-0.15980.0708-0.0198-0.0703-0.0219-0.01760.2519-0.0396-0.08180.20510.03650.0369-10.176-17.99831.724
20.93690.85590.16344.5336-0.69950.9871-0.10860.0679-0.0892-0.1353-0.027-0.455-0.07760.30560.13560.2649-0.1105-0.04520.31430.02410.103311.112-3.95735.015
34.30490.54130.29381.40620.23071.57970.1424-0.7520.3760.133-0.03730.03150.081-0.1241-0.10510.1873-0.0086-0.0460.3401-0.04340.062117.411-60.37841.986
44.9908-1.34620.67541.5961-0.63020.8712-0.0711-0.2630.81480.1062-0.0202-0.0707-0.15530.09320.09130.2093-0.0401-0.05470.2795-0.08340.171940.757-50.62639.171
50.9611-0.09710.67321.05130.03213.03740.01880.0383-0.0129-0.0051-0.00710.0023-0.09960.2376-0.01170.1383-0.0071-0.02860.20960.04920.019527.163-50.512-6.916
62.7767-2.9159-0.78253.21170.7040.56670.06450.071-0.5538-0.0329-0.09340.61320.27380.01440.02890.43050.0336-0.0980.28360.02750.225528.382-75.918-4.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 350
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION1A501 - 565
4X-RAY DIFFRACTION1B214
5X-RAY DIFFRACTION2B40 - 173
6X-RAY DIFFRACTION3C37 - 350
7X-RAY DIFFRACTION3C401 - 403
8X-RAY DIFFRACTION3C501 - 547
9X-RAY DIFFRACTION4D40 - 173
10X-RAY DIFFRACTION4D201 - 216
11X-RAY DIFFRACTION4E525
12X-RAY DIFFRACTION5E38 - 350
13X-RAY DIFFRACTION5E401 - 403
14X-RAY DIFFRACTION5F211
15X-RAY DIFFRACTION6F40 - 173
16X-RAY DIFFRACTION6F201 - 210

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