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

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Basic information

Entry
Database: PDB / ID: 5tqs
TitlePhospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the receptor tyrosine kinase ErbB2
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
  • Receptor protein-tyrosine kinaseReceptor tyrosine kinase
KeywordsHYDROLASE / SH2 / phospholipase / phosphopeptide
Function / homology
Function and homology information


calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / phospholipid catabolic process / phosphatidylinositol metabolic process ...calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / phospholipid catabolic process / phosphatidylinositol metabolic process / semaphorin receptor complex / phosphatidylinositol phospholipase C activity / COP9 signalosome / regulation of microtubule-based process / ErbB-3 class receptor binding / phosphatidylinositol-mediated signaling / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / positive regulation of Rho protein signal transduction / ERBB2-EGFR signaling pathway / neuromuscular junction development / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / positive regulation of epithelial cell migration / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / positive regulation of cell adhesion / cellular response to vascular endothelial growth factor stimulus / regulation of angiogenesis / coreceptor activity / Schwann cell development / release of sequestered calcium ion into cytosol / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / ruffle / myelination / Downregulation of ERBB2:ERBB3 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / neurogenesis / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / guanyl-nucleotide exchange factor activity / basal plasma membrane / regulation of ERK1 and ERK2 cascade / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of epithelial cell proliferation / Signaling by ERBB2 TMD/JMD mutants / neuromuscular junction / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / receptor protein-tyrosine kinase / neuron differentiation / cellular response to growth factor stimulus / ruffle membrane / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / lamellipodium / presynaptic membrane / myelin sheath / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / in utero embryonic development / positive regulation of MAPK cascade / membrane => GO:0016020 / cell surface receptor signaling pathway / receptor complex / early endosome / endosome membrane
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 / 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. ...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 / 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 / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / SH2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / SHC Adaptor Protein / 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 / Growth factor receptor cysteine-rich domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / SH2 domain superfamily / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2 / Receptor tyrosine-protein kinase erbB-2 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.876 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 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
E: Receptor protein-tyrosine kinase
F: Receptor protein-tyrosine kinase
H: Receptor protein-tyrosine kinase
G: Receptor protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)53,9808
Polymers53,9808
Non-polymers00
Water4,666259
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
E: Receptor protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)13,4952
Polymers13,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area6200 Å2
MethodPISA
2
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
F: Receptor protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)13,4952
Polymers13,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area6380 Å2
MethodPISA
3
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
G: Receptor protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)13,4952
Polymers13,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-6 kcal/mol
Surface area6380 Å2
MethodPISA
4
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
H: Receptor protein-tyrosine kinase


Theoretical massNumber of molelcules
Total (without water)13,4952
Polymers13,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.320, 30.620, 104.570
Angle α, β, γ (deg.)90.000, 100.120, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4 / Fragment: UNP residues 663-759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (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
Receptor protein-tyrosine kinase / Receptor tyrosine kinase


Mass: 1505.434 Da / Num. of mol.: 4 / Fragment: UNP residues 942-952 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B4DTR1, UniProt: P04626*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate (pH 5.5), 22% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.876→64.304 Å / Num. obs: 33698 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.07 Å2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.102 / Rsym value: 0.086 / Net I/av σ(I): 4.902 / Net I/σ(I): 9.1 / Num. measured all: 112903
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.876-1.982.80.4331.5196.3
1.98-2.13.10.2892.3199.1
2.1-2.243.60.1923.5199.4
2.24-2.423.60.1394.9199.5
2.42-2.653.60.1026.4199.6
2.65-2.973.60.0847.6199.6
2.97-3.433.50.0698.5199.7
3.43-4.23.40.0688199.8
4.2-5.933.30.0697.8199.5
5.93-64.3043.20.0578.6199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.88 Å64.3 Å
Translation1.88 Å64.3 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K44

4k44


Resolution: 1.876→51.472 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.237 1684 5 %
Rwork0.1885 --
obs0.1909 33684 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.7 Å2 / Biso mean: 36.9937 Å2 / Biso min: 9.6 Å2
Refinement stepCycle: final / Resolution: 1.876→51.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 0 268 3799
Biso mean---36.12 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073623
X-RAY DIFFRACTIONf_angle_d0.824875
X-RAY DIFFRACTIONf_chiral_restr0.049479
X-RAY DIFFRACTIONf_plane_restr0.005625
X-RAY DIFFRACTIONf_dihedral_angle_d15.5332171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8762-1.93140.29991300.26062505263594
1.9314-1.99380.31491390.23252618275798
1.9938-2.0650.28581390.21692637277699
2.065-2.14770.2511380.2042628276699
2.1477-2.24550.23081410.19732677281899
2.2455-2.36380.2551400.20222663280399
2.3638-2.51190.28951400.1962653279399
2.5119-2.70590.22631390.19432658279799
2.7059-2.97820.24421430.19672703284699
2.9782-3.4090.20051430.176327192862100
3.409-4.29470.22661430.156527162859100
4.2947-51.49090.22251490.18712823297299

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