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- PDB-6n9g: Crystal Structure of RGS7-Gbeta5 dimer -

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Basic information

Entry
Database: PDB / ID: 6n9g
TitleCrystal Structure of RGS7-Gbeta5 dimer
Components
  • Guanine nucleotide-binding protein subunit beta-5
  • Regulator of G-protein signaling 7
KeywordsSIGNALING PROTEIN / RGS / G protein SIGNALING
Function / homology
Function and homology information


G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / dark adaptation ...G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / dark adaptation / light adaption / G-protein gamma-subunit binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / negative regulation of voltage-gated calcium channel activity / G-protein activation / G alpha (s) signalling events / G alpha (12/13) signalling events / Ca2+ pathway / G alpha (q) signalling events / Extra-nuclear estrogen signaling / Vasopressin regulates renal water homeostasis via Aquaporins / rod photoreceptor outer segment / GPER1 signaling / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cell tip / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / ADP signalling through P2Y purinoceptor 1 / regulation of G protein-coupled receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G protein-coupled dopamine receptor signaling pathway / negative regulation of G protein-coupled receptor signaling pathway / G alpha (i) signalling events / parallel fiber to Purkinje cell synapse / G-protein alpha-subunit binding / photoreceptor inner segment / GTPase activator activity / myelin sheath / presynapse / protein-folding chaperone binding / presynaptic membrane / postsynaptic membrane / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / synapse / dendrite / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #60 / Regulator of G-protein signalling, DHEX domain / : / : / Regulator of G-protein signalling DHEX domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. ...Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #60 / Regulator of G-protein signalling, DHEX domain / : / : / Regulator of G-protein signalling DHEX domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Arc Repressor Mutant, subunit A / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 7 / Guanine nucleotide-binding protein subunit beta-5
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.129 Å
AuthorsPatil, D.N. / Rangarajan, E. / Izard, T. / Martemyanov, K.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA036596 United States
CitationJournal: Elife / Year: 2018
Title: Structural organization of a major neuronal G protein regulator, the RGS7-G beta 5-R7BP complex.
Authors: Patil, D.N. / Rangarajan, E.S. / Novick, S.J. / Pascal, B.D. / Kojetin, D.J. / Griffin, P.R. / Izard, T. / Martemyanov, K.A.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of G-protein signaling 7
B: Regulator of G-protein signaling 7
C: Guanine nucleotide-binding protein subunit beta-5
D: Guanine nucleotide-binding protein subunit beta-5


Theoretical massNumber of molelcules
Total (without water)187,0814
Polymers187,0814
Non-polymers00
Water8,629479
1
A: Regulator of G-protein signaling 7
D: Guanine nucleotide-binding protein subunit beta-5


Theoretical massNumber of molelcules
Total (without water)93,5402
Polymers93,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-51 kcal/mol
Surface area34660 Å2
MethodPISA
2
B: Regulator of G-protein signaling 7
C: Guanine nucleotide-binding protein subunit beta-5


Theoretical massNumber of molelcules
Total (without water)93,5402
Polymers93,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-55 kcal/mol
Surface area34780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.323, 162.760, 95.295
Angle α, β, γ (deg.)90.00, 98.36, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Regulator of G-protein signaling 7 / RGS7


Mass: 54761.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RGS7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O46470
#2: Protein Guanine nucleotide-binding protein subunit beta-5 / Gbeta5 / Transducin beta chain 5


Mass: 38778.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnb5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62881
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.25
Details: 0.1M sodium malonate (pH 6.25) and 10% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.129→94.28 Å / Num. obs: 54345 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.039 / Net I/σ(I): 14.6
Reflection shellResolution: 2.13→2.48 Å / Rmerge(I) obs: 0.817 / Num. unique obs: 2718 / CC1/2: 0.546 / Rpim(I) all: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBI

2pbi


Resolution: 2.129→37.535 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.93
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2610 4.8 %RANDOM
Rwork0.1743 ---
obs0.1764 54330 46.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.129→37.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12040 0 0 480 12520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212336
X-RAY DIFFRACTIONf_angle_d0.48816690
X-RAY DIFFRACTIONf_dihedral_angle_d17.8197421
X-RAY DIFFRACTIONf_chiral_restr0.041783
X-RAY DIFFRACTIONf_plane_restr0.0032160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1286-2.16730.450860.296175X-RAY DIFFRACTION1
2.1673-2.2090.393560.3621103X-RAY DIFFRACTION2
2.209-2.2540.342550.3634149X-RAY DIFFRACTION3
2.254-2.3030.442690.3113250X-RAY DIFFRACTION4
2.303-2.35660.4515260.35425X-RAY DIFFRACTION7
2.3566-2.41550.3557270.3133634X-RAY DIFFRACTION11
2.4155-2.48080.3497400.2865906X-RAY DIFFRACTION15
2.4808-2.55380.3702560.30871206X-RAY DIFFRACTION21
2.5538-2.63620.3421820.29071573X-RAY DIFFRACTION27
2.6362-2.73040.32191000.28431940X-RAY DIFFRACTION33
2.7304-2.83970.27011400.26482486X-RAY DIFFRACTION43
2.8397-2.96890.31251500.25083516X-RAY DIFFRACTION60
2.9689-3.12530.29991990.23474242X-RAY DIFFRACTION72
3.1253-3.3210.282620.21595058X-RAY DIFFRACTION86
3.321-3.57730.23593030.18865727X-RAY DIFFRACTION99
3.5773-3.93690.22173090.16125831X-RAY DIFFRACTION100
3.9369-4.50580.16952670.13075852X-RAY DIFFRACTION100
4.5058-5.67370.1683140.13485849X-RAY DIFFRACTION100
5.6737-37.54040.19083090.16645898X-RAY DIFFRACTION99
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)
12.9999-1.27051.34974.868-1.77731.97950.0112-0.48890.50580.5727-0.01950.6145-0.0152-0.47070.07740.3698-0.03760.14740.3095-0.09940.589310.766329.04255.8063
22.593-0.33840.12761.63-1.02995.01230.02780.22720.066-0.1462-0.07470.37980.1989-0.8274-0.20670.2877-0.0123-0.04870.37610.02060.53111.832332.1282-15.6674
30.9297-0.3296-0.50271.5538-0.8281.1080.0546-0.1822-0.05450.1568-0.0567-0.06190.2823-0.00370.04120.5225-0.0828-0.13360.2146-0.03850.379129.4388-0.84275.7866
41.50340.15950.382.95442.05873.97140.0775-0.1492-0.20690.07510.0262-0.8617-0.0277-0.2203-0.10920.37960.0036-0.22330.19420.08220.639750.3827-18.92832.3093
53.1647-1.69082.36922.5016-0.56693.99830.52870.49560.0874-0.2478-0.6077-1.08830.20441.17450.14920.9530.03380.32531.0790.52351.623340.840636.9038-45.3927
60.58440.1241-0.34814.9356-2.99743.7675-0.02920.51150.7826-0.689-0.3538-1.31370.27930.47310.33460.59090.04390.17030.57760.33841.062633.091528.2588-35.9387
70.7605-0.489-0.23981.34670.0171.8586-0.14050.22760.2159-0.4818-0.2898-0.4835-0.27130.0350.44420.6677-0.0866-0.08640.50130.23190.825815.708252.7988-48.432
84.91711.42991.59153.9422-0.50582.4644-0.3871-0.2850.35570.26180.1724-0.1269-0.4913-0.4210.21610.96020.2035-0.32360.59120.020.5926-12.567376.152-48.589
91.326-0.4130.45321.26090.30432.384-0.2510.38640.1634-0.3863-0.2687-0.5468-0.40170.03260.34570.6460.0016-0.20970.32010.19340.71079.69554.8294-47.6758
104.8425-0.4497-0.65136.4556-0.74776.2052-0.2169-0.0150.1003-0.47460.00390.40210.0062-0.64440.12540.6044-0.0068-0.2720.38120.00270.378-5.54849.8295-42.0136
111.43080.1501-0.03872.0539-0.41411.8708-0.14310.69490.1311-0.8998-0.5068-1.1558-0.20470.330.31150.88070.0231-0.04310.36750.35140.889814.435155.9221-47.6855
121.9150.4661-0.14712.4789-0.16020.81240.12420.0450.01890.0123-0.108-0.2703-0.07150.03920.03450.28890.01-0.11180.160.0240.241430.1886-0.1755-4.9594
132.1174-0.6058-1.93244.77981.18425.23150.3478-0.0379-0.41110.0118-0.15260.18450.34760.08-0.1690.4001-0.085-0.15090.14880.03820.248228.9446-9.5314-8.3393
141.8645-0.6907-0.1322.5725-0.22271.33410.046-0.20750.06290.387-0.0802-0.04670.08-0.12610.01330.3154-0.0702-0.06220.17230.0010.236727.1124.90194.2346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 317 )
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 450 )
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 182 )
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 317 )
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 450 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 118 )
10X-RAY DIFFRACTION10chain 'C' and (resid 119 through 216 )
11X-RAY DIFFRACTION11chain 'C' and (resid 217 through 353 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 172 )
13X-RAY DIFFRACTION13chain 'D' and (resid 173 through 216 )
14X-RAY DIFFRACTION14chain 'D' and (resid 217 through 353 )

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