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- PDB-6am3: Regulator of G protein signaling (RGS) 17 in complex with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 6am3
TitleRegulator of G protein signaling (RGS) 17 in complex with Ca2+
ComponentsRegulator of G-protein signaling 17
KeywordsSIGNALING PROTEIN / G protein / regulator / signaling
Function / homology
Function and homology information


negative regulation of signal transduction / response to amphetamine / GTPase activator activity / G alpha (z) signalling events / G alpha (i) signalling events / G alpha (q) signalling events / neuron projection / G protein-coupled receptor signaling pathway / GTPase activity / synapse ...negative regulation of signal transduction / response to amphetamine / GTPase activator activity / G alpha (z) signalling events / G alpha (i) signalling events / G alpha (q) signalling events / neuron projection / G protein-coupled receptor signaling pathway / GTPase activity / synapse / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Regulator of G-protein signaling 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSieng, M. / Lyon, A.M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: High-resolution structure of RGS17 suggests a role for Ca2+in promoting the GTPase-activating protein activity by RZ subfamily members.
Authors: Sieng, M. / Hayes, M.P. / O'Brien, J.B. / Andrew Fowler, C. / Houtman, J.C. / Roman, D.L. / Lyon, A.M.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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
X: Regulator of G-protein signaling 17
A: Regulator of G-protein signaling 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2109
Polymers32,5112
Non-polymers6997
Water5,278293
1
X: Regulator of G-protein signaling 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6805
Polymers16,2551
Non-polymers4254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulator of G-protein signaling 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5304
Polymers16,2551
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.571, 59.295, 65.337
Angle α, β, γ (deg.)90.000, 100.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 72 - 202 / Label seq-ID: 3 - 133

Dom-IDAuth asym-IDLabel asym-ID
1XA
2AB

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Components

#1: Protein Regulator of G-protein signaling 17 / RGS17


Mass: 16255.423 Da / Num. of mol.: 2 / Fragment: UNP residues 72-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS17, RGSZ2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGC6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M MES, pH 6.0, 22% PEG3350

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 8, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 39255 / % possible obs: 87.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.061 / Rrim(I) all: 0.146 / Χ2: 0.749 / Net I/σ(I): 4.6 / Num. measured all: 190012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.561.70.6659210.580.5170.8465.15841.4
1.56-1.581.80.54311870.5610.4370.70.39252.6
1.58-1.6220.55513780.6430.4120.6960.44462.4
1.62-1.652.20.60615530.620.4110.7380.42269.3
1.65-1.682.40.65417630.6610.4230.7850.39879.7
1.68-1.722.70.76819610.1170.4830.9140.74886.8
1.72-1.773.30.65220690.7550.3650.7530.41693.7
1.77-1.813.90.59421450.8230.3120.6740.42996.8
1.81-1.874.50.57422180.850.2830.6430.43997.7
1.87-1.935.10.50421670.8710.2390.560.46297.7
1.93-25.10.40521440.9160.1920.450.50795.6
2-2.084.90.31620650.9220.1580.3550.54492.2
2.08-2.176.20.25621970.9680.1120.280.54798.6
2.17-2.296.40.22122110.9780.0950.2410.62698.7
2.29-2.436.30.16622140.9820.0720.1820.63298.5
2.43-2.626.30.13522270.9890.0590.1470.68598.5
2.62-2.886.40.14221900.9920.060.1550.89398.2
2.88-3.36.40.08222310.9950.0350.0890.91397.9
3.3-4.156.10.06220930.9960.0270.0681.31992.9
4.15-507.20.05623210.9970.0220.061.29899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZV4

1zv4


Resolution: 1.53→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.698 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1938 4.9 %RANDOM
Rwork0.2033 ---
obs0.2043 37292 87.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 50.81 Å2 / Biso mean: 17.441 Å2 / Biso min: 9.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20.58 Å2
2--0.16 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.53→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 40 293 2570
Biso mean--37.24 28.15 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192364
X-RAY DIFFRACTIONr_bond_other_d0.0010.022177
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9733186
X-RAY DIFFRACTIONr_angle_other_deg0.92935089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4985282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02824.331127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0415443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7571519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
Refine LS restraints NCS

Ens-ID: 1 / Number: 9392 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1X
2A
LS refinement shellResolution: 1.533→1.573 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 77 -
Rwork0.305 1430 -
all-1507 -
obs--46.03 %
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)
10.63830.29180.77731.80641.32692.76180.0355-0.036-0.026-0.00740.0228-0.08030.10710.0529-0.05840.1540.0057-0.02330.00830.00220.0129-8.9442.0622-20.8145
21.2041-0.8017-0.93541.9121.16141.91980.06280.02550.05680.0020.0133-0.1003-0.040.078-0.07610.1684-0.0113-0.04380.00970.00270.0179-11.3409-21.6622-8.5247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X72 - 206
2X-RAY DIFFRACTION2A72 - 203

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