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Yorodumi- PDB-4gnk: Crystal structure of Galphaq in complex with full-length human PL... -
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-Basic information
Entry | Database: PDB / ID: 4gnk | ||||||
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Title | Crystal structure of Galphaq in complex with full-length human PLCbeta3 | ||||||
Components |
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Keywords | GTP-BINDING PROTEIN/HYDROLASE / GTP-binding protein alpha subunits / phospholipase C beta / coiled-coil domain / PH DOMAIN / EF HAND / C2 DOMAIN / TIM BARREL DOMAIN / phospholipase / GTP hydrolysis / G-protein signaling / membrane targeting / lipase / hydrolase / calcium binding / GTP binding / phospholipids / GTP-BINDING PROTEIN-HYDROLASE complex | ||||||
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 / G alpha (q) signalling events / Acetylcholine regulates insulin secretion / 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 / ADP signalling through P2Y purinoceptor 1 / regulation of systemic arterial blood pressure / regulation of platelet activation / phosphatidylinositol phospholipase C activity / phospholipase C activity / maternal behavior / glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / embryonic digit morphogenesis / postsynaptic cytosol / neuron remodeling / Synthesis of IP3 and IP4 in the cytosol / action potential / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / phosphatidylinositol-mediated signaling / enzyme regulator activity / lipid catabolic process / release of sequestered calcium ion into cytosol / GTPase activator activity / positive regulation of smooth muscle cell proliferation / G protein activity / post-embryonic development / skeletal system development / molecular function activator activity / caveola / G protein-coupled receptor binding / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / Ca2+ pathway / heart development / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / nuclear membrane / G alpha (q) signalling events / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / synapse / dendrite / calcium ion binding / negative regulation of apoptotic process / protein-containing complex binding / GTP binding / Golgi apparatus / protein-containing complex / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Lyon, A.M. / Tesmer, J.J.G. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2013 Title: Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain. Authors: Angeline M Lyon / Somnath Dutta / Cassandra A Boguth / Georgios Skiniotis / John J G Tesmer / Abstract: Phospholipase C-β (PLCβ) is directly activated by Gαq, but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present ...Phospholipase C-β (PLCβ) is directly activated by Gαq, but the molecular basis for how its distal C-terminal domain (CTD) contributes to maximal activity is poorly understood. Herein we present both the crystal structure and cryo-EM three-dimensional reconstructions of human full-length PLCβ3 in complex with mouse Gαq. The distal CTD forms an extended monomeric helical bundle consisting of three antiparallel segments with structural similarity to membrane-binding bin-amphiphysin-Rvs (BAR) domains. Sequence conservation of the distal CTD suggests putative membrane and protein interaction sites, the latter of which bind the N-terminal helix of Gαq in both the crystal structure and cryo-EM reconstructions. Functional analysis suggests that the distal CTD has roles in membrane targeting and in optimizing the orientation of the catalytic core at the membrane for maximal rates of lipid hydrolysis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gnk.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4gnk.ent.gz | 845.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gnk_validation.pdf.gz | 960.5 KB | Display | wwPDB validaton report |
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Full document | 4gnk_full_validation.pdf.gz | 985.2 KB | Display | |
Data in XML | 4gnk_validation.xml.gz | 81.5 KB | Display | |
Data in CIF | 4gnk_validation.cif.gz | 109.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/4gnk ftp://data.pdbj.org/pub/pdb/validation_reports/gn/4gnk | HTTPS FTP |
-Related structure data
Related structure data | 2271C 5561C 3ohm S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 41538.215 Da / Num. of mol.: 2 / Fragment: UNP residues 7-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: g alpha q, Gnaq / Plasmid: pFastBacDual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21279 |
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-1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta- ... , 2 types, 3 molecules BDE
#2: Protein | Mass: 139317.906 Da / Num. of mol.: 2 / Fragment: UNP residues 10-1234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: phospholipase c beta 3, PLCB3 / Plasmid: pFastBacDual / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q01970, phosphoinositide phospholipase C #3: Protein | | Mass: 30347.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: phospholipase c beta 3, PLCB3 / Plasmid: pFastBacDual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q01970 |
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-Non-polymers , 5 types, 14 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAIN E IS MOST LIKELY A C-TERMINAL PART OF EITHER CHAIN B OR CHAIN D IN THE CRYSTAL STRUCTURE. ...CHAIN E IS MOST LIKELY A C-TERMINAL PART OF EITHER CHAIN B OR CHAIN D IN THE CRYSTAL STRUCTURE. THERE IS NOT ENOUGH ELECTRON DENSITY TO ASSIGN IT TO CHAIN B OR CHAIN D. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.98 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 100 mM MES pH 6.75, 100-200 mM NaCl, and 11-12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 4→20 Å / Num. all: 41201 / Num. obs: 34695 / % possible obs: 76.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8 | ||||||||||||||||||
Reflection shell | Resolution: 4→4.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 1.9 / % possible all: 36.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OHM 3ohm Resolution: 4→19.99 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / SU B: 102.082 / SU ML: 0.575 / Cross valid method: THROUGHOUT / ESU R Free: 0.88 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.58 Å2
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Refinement step | Cycle: LAST / Resolution: 4→19.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 4→4.1 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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