[English] 日本語
Yorodumi
- PDB-7sq2: Reprocessed and refined structure of Phospholipase C-beta and Gq ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sq2
TitleReprocessed and refined structure of Phospholipase C-beta and Gq signaling complex
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
  • Guanine nucleotide-binding protein G(q) subunit alpha
KeywordsSIGNALING PROTEIN / G-protein signaling Phopholipase-C Hydrolase Guanine nucleotide-binding protein G(q) alpha
Function / homology
Function and homology information


Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / G alpha (q) signalling events / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / phosphatidylinositol metabolic process / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / regulation of platelet activation / ADP signalling through P2Y purinoceptor 1 / regulation of systemic arterial blood pressure / maternal behavior / phosphatidylinositol phospholipase C activity / phospholipase C activity / glutamate receptor signaling pathway / phosphatidylinositol-mediated signaling / regulation of canonical Wnt signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / postsynaptic cytosol / action potential / neuron remodeling / embryonic digit morphogenesis / Synthesis of IP3 and IP4 in the cytosol / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / enzyme regulator activity / lipid catabolic process / release of sequestered calcium ion into cytosol / GTPase activator activity / post-embryonic development / G protein activity / skeletal system development / molecular function activator activity / G protein-coupled receptor binding / caveola / positive regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / regulation of blood pressure / heterotrimeric G-protein complex / cell body / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (q) signalling events / nuclear membrane / protein stabilization / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / calcium ion binding / protein-containing complex binding / GTP binding / negative regulation of apoptotic process / Golgi apparatus / protein-containing complex / membrane / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family ...Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / 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 / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(q) subunit alpha / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEndo-Streeter, S.T. / Sondek, J. / Harden, T.K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM38213 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57391 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61454 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074001 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY010582 United States
CitationJournal: Science / Year: 2010
Title: Kinetic Scaffolding Mediated by a Phospholipase C-{beta} and Gq Signaling Complex
Authors: Endo-Streeter, S.T. / Sondek, J. / Harden, T.K.
History
DepositionNov 4, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2021ID: 3OHM
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,17014
Polymers138,1222
Non-polymers1,04812
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-53 kcal/mol
Surface area47110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.837, 90.817, 93.135
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein alpha-q


Mass: 38256.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21279
#2: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 / Phosphoinositide phospholipase C-beta-3 / Phospholipase C-beta-3 / PLC-beta-3


Mass: 99865.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q01970, phosphoinositide phospholipase C

-
Non-polymers , 6 types, 227 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG 6000, 100 mM Hepes, 1 mM CaCl2, 100 mM magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2010 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagittally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40.55 Å / Num. obs: 48454 / % possible obs: 99.49 % / Redundancy: 5.6 % / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Χ2: 1.804 / Net I/σ(I): 32.5
Reflection shellResolution: 2.6→2.666 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2555 / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.304 / Rrim(I) all: 0.723 / Χ2: 0.957 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OHM

3ohm
PDB Unreleased entry


Resolution: 2.6→40.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 29.23 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26334 2571 5 %RANDOM
Rwork0.19924 ---
obs0.20247 48454 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.472 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.51 Å2
2--5.24 Å2-0 Å2
3----6.06 Å2
Refinement stepCycle: 1 / Resolution: 2.6→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8678 0 64 215 8957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138920
X-RAY DIFFRACTIONr_bond_other_d00.0178322
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.65612069
X-RAY DIFFRACTIONr_angle_other_deg0.9591.57619316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.43451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.07822.008503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.139151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191570
X-RAY DIFFRACTIONr_chiral_restr0.0560.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.029875
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021907
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_it4.9793.7994291
X-RAY DIFFRACTIONr_mcbond_other4.9383.7884283
X-RAY DIFFRACTIONr_mcangle_it7.0545.6785348
X-RAY DIFFRACTIONr_mcangle_other7.0545.6785349
X-RAY DIFFRACTIONr_scbond_it5.9594.2394629
X-RAY DIFFRACTIONr_scbond_other5.964.244630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3586.1846722
X-RAY DIFFRACTIONr_long_range_B_refined12.74145.289963
X-RAY DIFFRACTIONr_long_range_B_other12.74145.299964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å
RfactorNum. reflection% reflection
Rfree0.34 203 -
Rwork0.274 3414 -
obs--95.59 %
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)
13.17490.5215-0.08121.55980.4333.2123-0.0331-0.13990.24020.14640.1612-0.00930.45630.5576-0.12810.7130.2249-0.52470.1395-0.14220.416910.727-4.54547.517
21.4566-0.2908-0.30390.8371-0.06183.60490.0751-0.03310.3093-0.2237-0.00260.0532-0.31060.4991-0.07250.62670.0189-0.48810.1446-0.11570.53926.68810.15713.269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 353
2X-RAY DIFFRACTION2B12 - 880

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more