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- PDB-5tq1: Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphop... -

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Basic information

Entry
Database: PDB / ID: 5tq1
TitlePhospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the insulin receptor
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
  • Insulin receptor
KeywordsHYDROLASE / SH2 / Phospholipase / phosphopeptide
Function / homology
Function and homology information


response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / IRS activation / : / 3-phosphoinositide-dependent protein kinase binding / yolk / embryonic liver development / cellular response to zinc ion starvation / Insulin receptor recycling ...response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / IRS activation / : / 3-phosphoinositide-dependent protein kinase binding / yolk / embryonic liver development / cellular response to zinc ion starvation / Insulin receptor recycling / phosphatidylinositol phospholipase C activity / Signal attenuation / phosphoinositide phospholipase C / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lipoic acid binding / positive regulation of glycoprotein biosynthetic process / negative regulation of glycogen biosynthetic process / response to resveratrol / phosphatidylinositol metabolic process / regulation of female gonad development / regulation of hydrogen peroxide metabolic process / positive regulation of meiotic cell cycle / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / COP9 signalosome / nuclear lumen / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / exocrine pancreas development / response to manganese ion / phospholipid catabolic process / response to vitamin D / dendritic spine maintenance / insulin binding / regulation of gluconeogenesis / adrenal gland development / cargo receptor activity / PTB domain binding / negative regulation of feeding behavior / response to starvation / response to food / response to testosterone / neuronal cell body membrane / phosphatidylinositol-mediated signaling / positive regulation of respiratory burst / amyloid-beta clearance / insulin receptor substrate binding / regulation of embryonic development / positive regulation of epithelial cell migration / positive regulation of receptor internalization / cellular response to vascular endothelial growth factor stimulus / response to tumor necrosis factor / positive regulation of phosphorylation / epidermis development / positive regulation of glycogen biosynthetic process / protein kinase activator activity / response to glucose / fat cell differentiation / heart morphogenesis / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / ruffle / release of sequestered calcium ion into cytosol / neuron projection maintenance / positive regulation of mitotic nuclear division / response to hormone / liver regeneration / guanyl-nucleotide exchange factor activity / dendrite membrane / response to glucocorticoid / receptor-mediated endocytosis / cellular response to epidermal growth factor stimulus / cerebellum development / positive regulation of glycolytic process / animal organ morphogenesis / response to activity / positive regulation of D-glucose import across plasma membrane / hippocampus development / liver development / receptor protein-tyrosine kinase / response to nutrient levels / response to insulin / receptor internalization / caveola / cellular response to growth factor stimulus / male gonad development / ruffle membrane / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of nitric oxide biosynthetic process / insulin receptor signaling pathway / late endosome / response to estradiol / nuclear envelope / lamellipodium / glucose homeostasis
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / : / PLCG EF-hand motif 1 / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / : / PLCG EF-hand motif 1 / PLCG EF-hand motif 2 / 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 C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Tyrosine-protein kinase, insulin-like receptor / SH2 domain / SHC Adaptor Protein / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Growth factor receptor cysteine-rich domain superfamily / SH3 domain / : / Fibronectin type 3 domain / SH2 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / Insulin receptor / Insulin receptor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.485 Å
AuthorsWuttke, D.S. / McKercher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1121842 United States
CitationJournal: Biochemistry / Year: 2017
Title: Multimodal Recognition of Diverse Peptides by the C-Terminal SH2 Domain of Phospholipase C-gamma 1 Protein.
Authors: McKercher, M.A. / Guan, X. / Tan, Z. / Wuttke, D.S.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
B: Insulin receptor


Theoretical massNumber of molelcules
Total (without water)13,3772
Polymers13,3772
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.010, 55.140, 58.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / PLC-148 / Phosphoinositide phospholipase C-gamma-1 / Phospholipase C-II / PLC-II / Phospholipase C- ...PLC-148 / Phosphoinositide phospholipase C-gamma-1 / Phospholipase C-II / PLC-II / Phospholipase C-gamma-1 / PLC-gamma-1


Mass: 11989.685 Da / Num. of mol.: 1 / Fragment: UNP residues 663-759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PLCG1 / Plasmid: pET15b / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P08487, phosphoinositide phospholipase C
#2: Protein/peptide Insulin receptor


Mass: 1387.340 Da / Num. of mol.: 1 / Fragment: UNP residues 9-19 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q9R1H1, UniProt: P15127*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Tris (pH 9.0), 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.485→58.665 Å / Num. all: 18758 / Num. obs: 18758 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 15.76 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/av σ(I): 7.218 / Net I/σ(I): 16.5 / Num. measured all: 104032
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.485-1.563.30.2232.2197.5
1.56-1.664.30.1434.7199.4
1.66-1.774.20.1016.6199.8
1.77-1.924.30.096.2199.9
1.92-2.14.30.0757.31100
2.1-2.358.60.0718.31100
2.35-2.718.50.06210199.9
2.71-3.328.20.069.6199.8
3.32-4.697.30.05211.81100
4.69-58.6657.10.04114.6198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å29.33 Å
Translation1.5 Å29.33 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K44

4k44


Resolution: 1.485→29.332 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.2099 929 4.97 %
Rwork0.1718 --
obs0.1736 18704 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.24 Å2 / Biso mean: 21.0886 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.485→29.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 170 1076
Biso mean---31.05 -
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004982
X-RAY DIFFRACTIONf_angle_d0.8341330
X-RAY DIFFRACTIONf_chiral_restr0.076133
X-RAY DIFFRACTIONf_plane_restr0.004175
X-RAY DIFFRACTIONf_dihedral_angle_d20.444387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4845-1.56280.26841190.21722432255197
1.5628-1.66070.24171350.19172483261899
1.6607-1.78890.22511280.185925432671100
1.7889-1.96890.22511350.183625062641100
1.9689-2.25370.21651340.162325482682100
2.2537-2.8390.19161370.174625782715100
2.839-29.33820.19931410.160726852826100

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