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- PDB-2bv1: Regulator of G-protein Signalling 1 (Human) -

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Basic information

Entry
Database: PDB / ID: 2bv1
TitleRegulator of G-protein Signalling 1 (Human)
ComponentsREGULATOR OF G-PROTEIN SIGNALLING 1
KeywordsSIGNALING PROTEIN / RGS1 / RGS / G-PROTEIN / REGULATOR / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / B-CELL ACTIVATION / PHOSPHORYLATION / SIGNAL TRANSDUCTION INHIBITOR
Function / homology
Function and homology information


leukotriene signaling pathway / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / GTPase activator activity / response to bacterium / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / G alpha (i) signalling events / G alpha (q) signalling events ...leukotriene signaling pathway / positive regulation of GTPase activity / G-protein alpha-subunit binding / negative regulation of signal transduction / GTPase activator activity / response to bacterium / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cytoplasmic side of plasma membrane / G alpha (i) signalling events / G alpha (q) signalling events / calmodulin binding / immune response / G protein-coupled receptor signaling pathway / GTPase activity / signal transduction / plasma membrane / cytosol
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 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 ...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 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulator of G-protein signaling 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsElkins, J.M. / Yang, X. / Soundararajan, M. / Schoch, G.A. / Haroniti, A. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Doyle, D.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / 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
DepositionJun 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF G-PROTEIN SIGNALLING 1
B: REGULATOR OF G-PROTEIN SIGNALLING 1


Theoretical massNumber of molelcules
Total (without water)33,1522
Polymers33,1522
Non-polymers00
Water2,792155
1
A: REGULATOR OF G-PROTEIN SIGNALLING 1


Theoretical massNumber of molelcules
Total (without water)16,5761
Polymers16,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: REGULATOR OF G-PROTEIN SIGNALLING 1


Theoretical massNumber of molelcules
Total (without water)16,5761
Polymers16,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.738, 43.202, 58.651
Angle α, β, γ (deg.)78.43, 85.30, 69.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A61 - 192
2114B61 - 192

NCS oper: (Code: given
Matrix: (-0.44716, -0.89413, -0.02396), (-0.89268, 0.4478, -0.05105), (0.05638, -0.00144, -0.99841)
Vector: -2.55667, 1.33661, -4.67071)

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Components

#1: Protein REGULATOR OF G-PROTEIN SIGNALLING 1 / RGS1 / EARLY RESPONSE PROTEIN 1R20 / B-CELL ACTIVATION PROTEIN BL34


Mass: 16575.793 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONEID 3916789
Plasmid: PLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08116
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINHIBITS SIGNAL TRANSDUCTION
Sequence detailsRESIDUES 48-49 OF CHAINS A, B ARE CLONING ARTEFACT

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 8
Details: 4.1M SODIUM FORMATE, 3% GLYCEROL. 1:1 MIXTURE WITH RGS1 PROTEIN AT 23MG/ML., pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 26, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.03 Å / Num. obs: 22497 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 65.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AGR AND 1FQJ

1agr

1fqj


Resolution: 2→57.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.626 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1170 5.2 %RANDOM
Rwork0.188 ---
obs0.191 21324 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0.41 Å20.41 Å2
2--0.26 Å20.05 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 0 155 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222150
X-RAY DIFFRACTIONr_bond_other_d0.0030.021896
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9542912
X-RAY DIFFRACTIONr_angle_other_deg0.89934424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56325.619105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69715376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.882157
X-RAY DIFFRACTIONr_chiral_restr0.090.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
X-RAY DIFFRACTIONr_nbd_refined0.2070.2511
X-RAY DIFFRACTIONr_nbd_other0.1660.21896
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21072
X-RAY DIFFRACTIONr_nbtor_other0.090.21157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0571.51485
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43522133
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3753918
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3684.5779
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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 / Number: 1887 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal0.732
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 42
Rwork0.232 983
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)
11.61180.0949-0.23183.59092.65514.22750.00960.1658-0.0364-0.25030.1164-0.13690.02880.0522-0.126-0.1439-0.0330.0194-0.11710.0478-0.1203-16.26083.7553-12.2985
23.1173-0.39761.40211.3197-0.37663.0430.0036-0.2742-0.02110.1862-0.00130.0751-0.01470.1675-0.0024-0.1065-0.02770.0558-0.1087-0.0068-0.07682.094818.03237.0573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 191
2X-RAY DIFFRACTION2B59 - 188

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