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- PDB-2a72: Structure of the regulator of G-protein signaling domain of RGS7 -

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Basic information

Entry
Database: PDB / ID: 2a72
TitleStructure of the regulator of G-protein signaling domain of RGS7
ComponentsRegulator of G-protein signalling 7
KeywordsSIGNALING PROTEIN / Human RGS7 / regulator of G-protein signaling 7 / GTPase-activating proteins (GAP) / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dendrite terminus / cell tip / negative regulation of G protein-coupled receptor signaling pathway / regulation of postsynaptic membrane potential / positive regulation of GTPase activity / G-protein alpha-subunit binding / GTPase activator activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / presynaptic membrane ...dendrite terminus / cell tip / negative regulation of G protein-coupled receptor signaling pathway / regulation of postsynaptic membrane potential / positive regulation of GTPase activity / G-protein alpha-subunit binding / GTPase activator activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / presynaptic membrane / G alpha (i) signalling events / postsynaptic membrane / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / glutamatergic synapse / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Regulator of G-protein signalling, DHEX domain / : / : / Regulator of G-protein signalling DHEX domain / 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 signalling, DHEX domain / : / : / Regulator of G-protein signalling DHEX domain / 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 / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchoch, G.A. / Johansson, C. / Phillips, C. / Debreczeni, J. / Smee, C. / Elkins, J.M. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / von Delft, F. ...Schoch, G.A. / Johansson, C. / Phillips, C. / Debreczeni, J. / Smee, C. / Elkins, J.M. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / von Delft, F. / Gileadi, O. / 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
DepositionJul 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source / _diffrn_source.type
Revision 1.4Feb 14, 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 / 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 / _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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: Two biological units are present in the asymmetric unit that are formed from the ...BIOMOLECULE: Two biological units are present in the asymmetric unit that are formed from the combinations of residues 320 to 414 of chain A with 415 to 450 of chain B and residues 320 to 414 of chain B with 415 to 450 of chain A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of G-protein signalling 7
B: Regulator of G-protein signalling 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3123
Polymers34,2772
Non-polymers351
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-56 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.915, 106.033, 52.490
Angle α, β, γ (deg.)90.00, 103.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 326 - 443 / Label seq-ID: 9 - 126

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Regulator of G-protein signalling 7


Mass: 17138.375 Da / Num. of mol.: 2 / Fragment: RESIDUES 320-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLIC-SGC / Production host: Escherichia coli (E. coli) / References: UniProt: P49802
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / 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: 2.1 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, (NH4)2SO4, BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.93 Å / Num. all: 19896 / Num. obs: 19896 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.079 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2457 / Rsym value: 0.536 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQJ_B.pdb

Resolution: 2→53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.269 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.195 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1028 5.2 %RANDOM
Rwork0.18425 ---
all0.18756 18842 --
obs0.18756 18842 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.5 Å2
2---1.7 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 1 231 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222239
X-RAY DIFFRACTIONr_bond_other_d0.0010.021983
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9573023
X-RAY DIFFRACTIONr_angle_other_deg0.85734627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9525268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21723.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined0.2140.2513
X-RAY DIFFRACTIONr_nbd_other0.1730.21879
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21099
X-RAY DIFFRACTIONr_nbtor_other0.0850.21113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6791.51395
X-RAY DIFFRACTIONr_mcbond_other0.1591.5532
X-RAY DIFFRACTIONr_mcangle_it0.95122156
X-RAY DIFFRACTIONr_scbond_it1.7613996
X-RAY DIFFRACTIONr_scangle_it2.7994.5865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
692medium positional0.180.5
1134loose positional0.625
692medium thermal0.442
1134loose thermal0.9610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 58 -
Rwork0.291 1084 -
obs--73.02 %
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)
10.38340.1271-0.62375.99621.63941.9808-0.0146-0.0002-0.1141-0.3795-0.0299-0.6755-0.0442-0.03920.0444-0.16950.00070.0455-0.10150.0331-0.06939.56712.387433.8216
21.34971.6077-0.612812.0316-8.15637.37170.1724-0.1943-0.04980.2661-0.13920.0585-0.09750.0245-0.0332-0.1966-0.037-0.0334-0.0805-0.0528-0.21246.4066-37.086241.7432
31.2146-0.36930.15255.0849-2.34562.4870.1117-0.02140.0353-0.2917-0.11760.08590.05290.12250.0059-0.1375-0.027-0.0324-0.1084-0.0433-0.20836.2798-35.128333.5945
41.091.98160.16869.91176.42176.69790.153-0.2499-0.14270.2433-0.2077-0.30990.0565-0.03070.0546-0.230.0021-0.0331-0.07020.0452-0.09988.68614.203741.949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA318 - 4131 - 96
2X-RAY DIFFRACTION2AA414 - 45097 - 133
3X-RAY DIFFRACTION3BB318 - 4131 - 96
4X-RAY DIFFRACTION4BB414 - 45097 - 133

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