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- PDB-1fqj: CRYSTAL STRUCTURE OF THE HETEROTRIMERIC COMPLEX OF THE RGS DOMAIN... -

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Entry
Database: PDB / ID: 1fqj
TitleCRYSTAL STRUCTURE OF THE HETEROTRIMERIC COMPLEX OF THE RGS DOMAIN OF RGS9, THE GAMMA SUBUNIT OF PHOSPHODIESTERASE AND THE GT/I1 CHIMERA ALPHA SUBUNIT [(RGS9)-(PDEGAMMA)-(GT/I1ALPHA)-(GDP)-(ALF4-)-(MG2+)]
Components
  • Guanine nucleotide-binding protein G(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1
  • Regulator of G-protein signaling 9
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
KeywordsSIGNALING PROTEIN / RGS9 / transducin / effector / PDEgamma / G Protein / Phototransduction / rod / RGS / phosphodiesterase / GAP
Function / homology
Function and homology information


sensory perception of umami taste / Extra-nuclear estrogen signaling / detection of light stimulus involved in visual perception / Adenylate cyclase inhibitory pathway / G protein-coupled receptor complex / 3',5'-cyclic-GMP phosphodiesterase / cellular response to electrical stimulus / photoreceptor connecting cilium / negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled adenosine receptor signaling pathway ...sensory perception of umami taste / Extra-nuclear estrogen signaling / detection of light stimulus involved in visual perception / Adenylate cyclase inhibitory pathway / G protein-coupled receptor complex / 3',5'-cyclic-GMP phosphodiesterase / cellular response to electrical stimulus / photoreceptor connecting cilium / negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled adenosine receptor signaling pathway / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / Activation of the phototransduction cascade / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / response to stimulus / Ca2+ pathway / acyl binding / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of synaptic transmission / positive regulation of G protein-coupled receptor signaling pathway / photoreceptor outer segment membrane / G alpha (i) signalling events / GTPase activating protein binding / ion binding / positive regulation of protein localization to cell cortex / cell cortex region / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / 3',5'-cyclic-GMP phosphodiesterase activity / response to light stimulus / cGMP binding / phototransduction / regulation of mitotic spindle organization / cellular response to forskolin / negative regulation of signal transduction / visual perception / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / photoreceptor disc membrane / photoreceptor inner segment / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / G protein-coupled receptor binding / retina development in camera-type eye / GDP binding / cell cortex / midbody / cell population proliferation / positive regulation of MAPK cascade / molecular adaptor activity / G protein-coupled receptor signaling pathway / intracellular signal transduction / cell cycle / cell division / centrosome / GTPase activity / membrane raft / GTP binding / protein kinase binding / magnesium ion binding / protein-containing complex / zinc ion binding / membrane / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like ...Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Regulator of G-protein Signalling 4; domain 1 - #10 / Regulator of G-protein Signalling 4; domain 1 / 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 / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Regulator of G-protein signaling 9 / Guanine nucleotide-binding protein G(t) subunit alpha-1 / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (cattle)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å
AuthorsSlep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B.
CitationJournal: Nature / Year: 2001
Title: Structural determinants for regulation of phosphodiesterase by a G protein at 2.0 A.
Authors: Slep, K.C. / Kercher, M.A. / He, W. / Cowan, C.W. / Wensel, T.G. / Sigler, P.B.
History
DepositionSep 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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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(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1
B: Regulator of G-protein signaling 9
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
D: Guanine nucleotide-binding protein G(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1
E: Regulator of G-protein signaling 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,26211
Polymers114,1215
Non-polymers1,1416
Water6,413356
1
A: Guanine nucleotide-binding protein G(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1
B: Regulator of G-protein signaling 9
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9106
Polymers59,3403
Non-polymers5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Guanine nucleotide-binding protein G(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1
E: Regulator of G-protein signaling 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3515
Polymers54,7812
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.609, 115.937, 134.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Guanine nucleotide-binding protein G(t) subunit alpha-1,Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(t) subunit alpha-1 / Transducin alpha-1 chain / Adenylate cyclase-inhibiting G alpha protein / Transducin alpha-1 chain


Mass: 37361.656 Da / Num. of mol.: 2
Fragment: UNP P04695 residues 26-215 and 295-350 linked via UNP P10824 residues 220-298
Source method: isolated from a genetically manipulated source
Details: THE CHIMERA COMPRISES RESIDUES 26 TO 215 OF BOVINE GT, RESIDUES 220 TO 298 OF RAT GI1, AND RESIDUES 295 TO 350 OF BOVINE GT
Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Rattus norvegicus (Norway rat)
Genus: Bos, Rattus / Species: , / Gene: GNAT1, Gnai1, Gnai-1 / Plasmid: PHIS6(T7) / Production host: Escherichia coli (E. coli) / References: UniProt: P04695, UniProt: P10824
#2: Protein Regulator of G-protein signaling 9 / RGS9


Mass: 17419.176 Da / Num. of mol.: 2 / Fragment: RGS DOMAIN UNP RESIDUES 276-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RGS9 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O46469

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma


Mass: 4559.094 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 46-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PDE6G, PDEG / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli)
References: UniProt: P04972, 3',5'-cyclic-GMP phosphodiesterase

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Non-polymers , 4 types, 362 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 15.0% PEG8000, 200mM Tris pH9.0, 0.2% beta-ME, 1mM (NH4)2WS4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215.5 %PEG80001reservoir
350 mMTris1reservoir
45 %ethylene glycol1reservoir
575 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: APS-1 / Detector: CCD / Date: Sep 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 2227054 / Num. obs: 93531 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.553 / Num. unique all: 2094 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 2227054 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.7 % / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.02→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2012134.44 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 17150 9.8 %RANDOM; 9.9%
Rwork0.233 ---
obs0.233 175158 96.8 %-
all-181077 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.33 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.77 Å20 Å20 Å2
2--8.75 Å20 Å2
3----3.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7683 0 68 356 8107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 2745 9.9 %
Rwork0.306 24934 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PARAM
X-RAY DIFFRACTION3ALF4.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.342 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.306 / Rfactor obs: 0.319

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