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- PDB-3c7k: Molecular architecture of Galphao and the structural basis for RG... -

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Basic information

Entry
Database: PDB / ID: 3c7k
TitleMolecular architecture of Galphao and the structural basis for RGS16-mediated deactivation
Components
  • Guanine nucleotide-binding protein G(o) subunit alpha
  • Regulator of G-protein signaling 16
KeywordsSIGNALING PROTEIN / RGS / Galpha / AlF4 heterotrimeric G-protein GAP / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Palmitate / Transducer / Phosphoprotein / Signal transduction inhibitor
Function / homology
Function and homology information


response to serotonin / G alpha (z) signalling events / potassium channel activator activity / Ca2+ pathway / G alpha (q) signalling events / G alpha (i) signalling events / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / GTPase activating protein binding / G protein-coupled dopamine receptor signaling pathway ...response to serotonin / G alpha (z) signalling events / potassium channel activator activity / Ca2+ pathway / G alpha (q) signalling events / G alpha (i) signalling events / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / GTPase activating protein binding / G protein-coupled dopamine receptor signaling pathway / regulation of heart contraction / negative regulation of calcium ion transport / parallel fiber to Purkinje cell synapse / positive regulation of GTPase activity / negative regulation of signal transduction / postsynaptic modulation of chemical synaptic transmission / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / GTPase activator activity / locomotory behavior / negative regulation of insulin secretion / GABA-ergic synapse / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / myelin sheath / heterotrimeric G-protein complex / synaptic vesicle membrane / cell body / G protein activity / presynaptic membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynaptic membrane / G protein-coupled receptor signaling pathway / signaling receptor binding / GTPase activity / dendrite / GTP binding / glutamatergic synapse / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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 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 / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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(o) subunit alpha / Regulator of G-protein signaling 16
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSlep, K.C. / Kercher, M.A. / Wieland, T. / Chen, C. / Simon, M.I. / Sigler, P.B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular architecture of G{alpha}o and the structural basis for RGS16-mediated deactivation.
Authors: Slep, K.C. / Kercher, M.A. / Wieland, T. / Chen, C.K. / Simon, M.I. / Sigler, P.B.
History
DepositionFeb 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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_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_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(o) subunit alpha
B: Regulator of G-protein signaling 16
C: Guanine nucleotide-binding protein G(o) subunit alpha
D: Regulator of G-protein signaling 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,57610
Polymers105,4354
Non-polymers1,1416
Water1086
1
A: Guanine nucleotide-binding protein G(o) subunit alpha
B: Regulator of G-protein signaling 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2885
Polymers52,7182
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Guanine nucleotide-binding protein G(o) subunit alpha
D: Regulator of G-protein signaling 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2885
Polymers52,7182
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.357, 96.357, 235.610
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, 4 molecules ACBD

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


Mass: 37854.863 Da / Num. of mol.: 2 / Fragment: Residues 22-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnao1, Gna0, Gnao / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P18872
#2: Protein Regulator of G-protein signaling 16 / RGS16 / Retinally abundant regulator of G-protein signaling / RGS-R / A28-RGS14P


Mass: 14862.650 Da / Num. of mol.: 2 / Fragment: Residues 53-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rgs16, Rgsr / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97428

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#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.: 6 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 8000 200 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.15 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 1, 1999 / Details: X25 Optics
RadiationMonochromator: X25 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 33119 / Num. obs: 27489 / % possible obs: 83 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 93.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 20.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AGR

1agr


Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 2365 8.2 %random
Rwork0.25 ---
obs-24012 83 %-
Solvent computationBsol: 37.083 Å2
Displacement parametersBiso mean: 87.344 Å2
Baniso -1Baniso -2Baniso -3
1--10.619 Å2-17.322 Å20 Å2
2---10.619 Å20 Å2
3---21.238 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6815 0 68 6 6889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.346
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3gdp.prm
X-RAY DIFFRACTION4alf4.prm
X-RAY DIFFRACTION5CNS_TOPPAR:ion.param

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