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- PDB-2v4z: The crystal structure of the human G-protein subunit alpha (GNAI3... -

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Basic information

Entry
Database: PDB / ID: 2v4z
TitleThe crystal structure of the human G-protein subunit alpha (GNAI3) in complex with an engineered regulator of G-protein signaling type 2 domain (RGS2)
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(K) SUBUNIT ALPHA
  • REGULATOR OF G-PROTEIN SIGNALING 2
KeywordsCELL CYCLE / GTP HYDROLYSIS / ADP-RIBOSYLATION / NUCLEOTIDE-BINDING / LIPOPROTEIN / GTP-BINDING / PHOSPHOPROTEIN / SIGNAL TRANSDUCTION INHIBITOR / GUANINE NUCLEOTIDE BINDING PROTEIN / TRANSMEMBRANE SIGNALING / G-PROTEIN COUPLED RECEPTOR / PALMITATE / MYRISTATE / TRANSDUCER
Function / homology
Function and homology information


negative regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / adenylate cyclase inhibitor activity / zymogen granule / ovulation / negative regulation of cardiac muscle hypertrophy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of NAD(P)H oxidase activity ...negative regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway involved in heart process / negative regulation of phospholipase activity / negative regulation of glycine import across plasma membrane / adenylate cyclase inhibitor activity / zymogen granule / ovulation / negative regulation of cardiac muscle hypertrophy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of NAD(P)H oxidase activity / regulation of G protein-coupled receptor signaling pathway / vesicle fusion / negative regulation of adenylate cyclase activity / relaxation of vascular associated smooth muscle / dopamine receptor signaling pathway / GTP metabolic process / beta-tubulin binding / relaxation of cardiac muscle / GTPase activating protein binding / brown fat cell differentiation / Adenylate cyclase inhibitory pathway / positive regulation of cardiac muscle contraction / G protein-coupled serotonin receptor binding / positive regulation of macroautophagy / G-protein alpha-subunit binding / maternal process involved in female pregnancy / negative regulation of apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cytoplasmic side of plasma membrane / ADP signalling through P2Y purinoceptor 12 / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / response to amphetamine / positive regulation of superoxide anion generation / G alpha (z) signalling events / GTPase activator activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of neuron projection development / GPER1 signaling / heterotrimeric G-protein complex / negative regulation of MAP kinase activity / ADORA2B mediated anti-inflammatory cytokines production / G protein-coupled receptor binding / GDP binding / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / midbody / brain development / spermatogenesis / Extra-nuclear estrogen signaling / negative regulation of translation / response to ethanol / calmodulin binding / lysosomal membrane / G protein-coupled receptor signaling pathway / cell cycle / cell division / neuron projection / centrosome / GTPase activity / membrane raft / protein domain specific binding / GTP binding / nucleolus / Golgi apparatus / mitochondrion / extracellular exosome / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Regulator of G-protein signalling 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain / RGS, subdomain 2 ...Regulator of G-protein signalling 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / P-loop containing nucleotide triphosphate hydrolases / 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 / Guanine nucleotide-binding protein G(i) subunit alpha-3 / Regulator of G-protein signaling 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRoos, A.K. / Soundararajan, M. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Determinants of G-Protein Alpha Subunit Selectivity by Regulator of G-Protein Signaling 2(Rgs2).
Authors: Kimple, A.J. / Soundararajan, M. / Hutsell, S.Q. / Roos, A.K. / Urban, D.J. / Setola, V. / Temple, B.R. / Roth, B.L. / Knapp, S. / Willard, F.S. / Siderovski, D.P.
History
DepositionSep 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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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(K) SUBUNIT ALPHA
B: REGULATOR OF G-PROTEIN SIGNALING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1945
Polymers56,6232
Non-polymers5703
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8.2 kcal/mol
Surface area24060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)114.539, 114.539, 99.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GUANINE NUCLEOTIDE-BINDING PROTEIN G(K) SUBUNIT ALPHA / G(I) ALPHA-3 / GUANINE NUCLEOTIDE-BINDING PROTEIN G K SUBUNIT ALPHA G I ALPHA-3


Mass: 40162.578 Da / Num. of mol.: 1 / Fragment: SUBUNIT ALPHA, RESIDUES 4-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P08754
#2: Protein REGULATOR OF G-PROTEIN SIGNALING 2 / G0/G1 SWITCH REGULATORY PROTEIN 8 / RGS2 / CELL GROWTH-INHIBITING GENE 31 PROTEIN


Mass: 16460.529 Da / Num. of mol.: 1 / Fragment: RGS DOMAIN, RESIDUES 71-209 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P41220

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Non-polymers , 4 types, 21 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, CYS 106 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 184 TO ASP ...ENGINEERED RESIDUE IN CHAIN B, CYS 106 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 184 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 191 TO LYS
Sequence detailsTRIPLE MUTANT C106S, N184D, E191K

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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: 3.47 Å3/Da / Density % sol: 64.6 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 2, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→35.09 Å / Num. obs: 18916 / % possible obs: 99.9 % / Observed criterion σ(I): 2.3 / Redundancy: 7.2 % / Biso Wilson estimate: 67.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IHB
Resolution: 2.8→33.37 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / SU B: 27.265 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 959 5.1 %RANDOM
Rwork0.208 ---
obs0.21 17941 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 34 18 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223495
X-RAY DIFFRACTIONr_bond_other_d0.0010.022285
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9544740
X-RAY DIFFRACTIONr_angle_other_deg0.78635553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15824.417163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46415561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7371518
X-RAY DIFFRACTIONr_chiral_restr0.0510.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2681.52177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52123478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7431318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2884.51262
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
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 60
Rwork0.329 1307
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.31470.4059-0.74452.5912-0.02233.0780.0873-0.1791-0.2075-0.0661-0.1899-0.2548-0.05860.20740.1026-0.3001-0.0007-0.0515-0.22770.032-0.3305-0.762445.7584-9.8955
24.8342-1.4769-2.20165.2818-1.9847.4831-0.1026-0.8716-0.31951.68980.16820.70530.16430.1155-0.06550.23550.0580.0820.23660.25390.0106-5.839336.129711.9945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 347
2X-RAY DIFFRACTION1A1348
3X-RAY DIFFRACTION1A1349
4X-RAY DIFFRACTION2B72 - 199

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