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- PDB-1agr: COMPLEX OF ALF4-ACTIVATED GI-ALPHA-1 WITH RGS4 -

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Basic information

Entry
Database: PDB / ID: 1agr
TitleCOMPLEX OF ALF4-ACTIVATED GI-ALPHA-1 WITH RGS4
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
  • RGS4
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/REGULATOR) / GI-ALPHA-1 / HYDROLASE / SIGNAL TRANSDUCTION / RGS4 / COMPLEX (SIGNAL TRANSDUCTION-REGULATOR) / GTP-BINDING / GTPASE ACTIVATING PROTEIN / COMPLEX (SIGNAL TRANSDUCTION-REGULATOR) complex
Function / homology
Function and homology information


negative regulation of glycine import across plasma membrane / negative regulation of dopamine receptor signaling pathway / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of potassium ion transmembrane transport / dorsal root ganglion development / negative regulation of cell growth involved in cardiac muscle cell development / regulation of actin filament organization / negative regulation of synaptic transmission / regulation of potassium ion transmembrane transport ...negative regulation of glycine import across plasma membrane / negative regulation of dopamine receptor signaling pathway / Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / negative regulation of potassium ion transmembrane transport / dorsal root ganglion development / negative regulation of cell growth involved in cardiac muscle cell development / regulation of actin filament organization / negative regulation of synaptic transmission / regulation of potassium ion transmembrane transport / GTPase activating protein binding / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / negative regulation of G protein-coupled receptor signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of calcium ion transport / G-protein alpha-subunit binding / positive regulation of excitatory postsynaptic potential / positive regulation of heart rate / positive regulation of protein localization to cell cortex / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / GTPase activator activity / regulation of mitotic spindle organization / response to amphetamine / response to cocaine / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / GDP binding / heterotrimeric G-protein complex / G protein activity / midbody / response to ethanol / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / postsynapse / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / protein kinase binding / GTP binding / glutamatergic synapse / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Regulator of G-protein signalling 4, RGS domain / 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 ...Regulator of G-protein signalling 4, RGS domain / 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 / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / CITRIC ACID / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Regulator of G-protein signaling 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, DENSITY MODIFICATION / Resolution: 2.8 Å
AuthorsTesmer, J.J.G. / Sprang, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis.
Authors: Tesmer, J.J. / Berman, D.M. / Gilman, A.G. / Sprang, S.R.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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(I)
D: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
E: RGS4
H: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,63412
Polymers127,1094
Non-polymers1,5258
Water1,04558
1
A: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
E: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3176
Polymers63,5552
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)
H: RGS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3176
Polymers63,5552
Non-polymers7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.000, 97.200, 110.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.964372, 0.208506, -0.162827), (0.207851, -0.97793, -0.021238), (-0.163661, -0.013363, -0.986426)
Vector: 7.7071, -25.6439, 61.2808)

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Components

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Protein , 2 types, 4 molecules ADEH

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(I) / GI-ALPHA-1


Mass: 40267.836 Da / Num. of mol.: 2 / Fragment: ALPHA-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Organ: BRAIN / Plasmid: PQE6/GIA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10824
#2: Protein RGS4 / REGULATOR OF G-PROTEIN SIGNALLING 4


Mass: 23286.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Organ: BRAIN / Plasmid: PQE60-H6RGS4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P49799

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Non-polymers , 5 types, 66 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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.3
Details: THE COMPLEX WAS CRYSTALLIZED IN HANGING DROPS USING PEG 10000 AS THE PRECIPITANT AND SODIUM CITRATE PH 5.3 AS THE BUFFER., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium citrate1reservoir
214.4 %(v/v)PEG100001reservoir
35 mMDTT1reservoir
40.140 mM1reservoirAlCl3
570 mM1reservoirNaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 43341 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rsym value: 0.12 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.55 / % possible all: 99.4
Reflection
*PLUS
Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
AVGSYSmodel building
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
AVGSYSphasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, DENSITY MODIFICATION
Starting model: PDB ENTRY 1GFI

1gfi


Resolution: 2.8→5 Å / Rfactor Rfree error: 0.0048 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: ALL BUT LAST ROUND / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3644 10 %RANDOM
Rwork0.216 ---
obs0.216 35475 99 %-
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7580 56 28 56 7720
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.60.5
X-RAY DIFFRACTIONx_mcangle_it5.81
X-RAY DIFFRACTIONx_scbond_it7.41
X-RAY DIFFRACTIONx_scangle_it10.91.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.05 Å / Weight position: 200
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.337 1331

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