[English] 日本語
Yorodumi
- PDB-6pbc: Structural basis for the activation of PLC-gamma isozymes by phos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pbc
TitleStructural basis for the activation of PLC-gamma isozymes by phosphorylation and cancer-associated mutations
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma,1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / 1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase gamma-1
Function / homology
Function and homology information


PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / phospholipid catabolic process / response to gravity / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / ruffle / response to organonitrogen compound / guanyl-nucleotide exchange factor activity / positive regulation of release of sequestered calcium ion into cytosol / cell projection / calcium-mediated signaling / phosphoprotein binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / insulin receptor binding / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / glutamatergic synapse / calcium ion binding / protein kinase binding / plasma membrane / cytosol / cytoplasm
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 C, X 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 / 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. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PH domain / C2 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 / SH2 domain superfamily / EF-hand calcium-binding domain. / 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 / PH-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.46 Å
AuthorsHajicek, N. / Sondek, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM057391 United States
CitationJournal: Elife / Year: 2019
Title: Structural basis for the activation of PLC-gamma isozymes by phosphorylation and cancer-associated mutations.
Authors: Hajicek, N. / Keith, N.C. / Siraliev-Perez, E. / Temple, B.R.S. / Huang, W. / Zhang, Q. / Harden, T.K. / Sondek, J.
History
DepositionJun 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma,1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0203
Polymers135,9571
Non-polymers632
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.766, 82.441, 228.318
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 135956.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1, rCG_32419, Plcg1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: G3V845, UniProt: P10686, phosphoinositide phospholipase C
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% w/v PEG 3,350, 50 mM di-sodium tartrate, 5% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 49513 / % possible obs: 99.6 % / Redundancy: 8.1 % / Biso Wilson estimate: 34.03 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.046 / Rrim(I) all: 0.132 / Χ2: 0.965 / Net I/σ(I): 6.8 / Num. measured all: 400272
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.46-2.56.80.69122570.8080.2810.7480.82592.3
2.5-2.557.60.6924290.8290.2670.7410.812100
2.55-2.68.20.62124630.8920.2280.6620.816100
2.6-2.658.30.55124380.9150.2020.5880.802100
2.65-2.718.30.47224330.9360.1730.5030.799100
2.71-2.778.30.41624590.9490.1520.4440.81100
2.77-2.848.30.34924650.960.1280.3720.801100
2.84-2.928.30.31624300.9720.1160.3370.83100
2.92-38.30.26624620.9770.0980.2840.845100
3-3.18.30.21524930.9840.0790.2290.853100
3.1-3.218.30.17424700.9890.0640.1850.915100
3.21-3.348.30.13624380.9940.050.1450.928100
3.34-3.498.20.11424850.9950.0420.1210.967100
3.49-3.678.20.09224800.9970.0340.0981.01100
3.67-3.98.20.0825170.9980.0290.0851.023100
3.9-4.218.20.0724930.9970.0260.0751.112100
4.21-4.638.10.06824930.9980.0250.0721.335100
4.63-5.380.07325360.9970.0270.0781.626100
5.3-6.6780.07425540.9970.0280.0791.192100
6.67-507.50.03827180.9990.0140.0410.94299.6

-
Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.09 Å41.22 Å
Translation8.09 Å41.22 Å
Phasing dmFOM : 0.77 / FOM acentric: 0.78 / FOM centric: 0.68 / Reflection: 27017 / Reflection acentric: 23851 / Reflection centric: 3166
Phasing dm shellResolution: 3→3.2 Å / FOM : 0.55 / FOM acentric: 0.56 / FOM centric: 0.48 / Reflection: 4303 / Reflection acentric: 4019 / Reflection centric: 284

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.46→41.22 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.02
RfactorNum. reflection% reflection
Rfree0.2447 3526 7.13 %
Rwork0.2018 --
obs0.2049 49437 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 352.42 Å2 / Biso mean: 41.2639 Å2 / Biso min: 18.64 Å2
Refinement stepCycle: final / Resolution: 2.46→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8598 0 2 246 8846
Biso mean--49.49 32.29 -
Num. residues----1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038806
X-RAY DIFFRACTIONf_angle_d0.58611916
X-RAY DIFFRACTIONf_chiral_restr0.0431285
X-RAY DIFFRACTIONf_plane_restr0.0041535
X-RAY DIFFRACTIONf_dihedral_angle_d14.4935286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4589-2.49260.32131110.25711758186996
2.4926-2.52820.30471400.260718441984100
2.5282-2.56590.29371410.246517671908100
2.5659-2.6060.29151290.246618361965100
2.606-2.64880.2771220.233518491971100
2.6488-2.69440.28981480.232517721920100
2.6944-2.74340.30541420.231618351977100
2.7434-2.79620.34231390.23717961935100
2.7962-2.85320.29741380.242518521990100
2.8532-2.91520.26961410.24417891930100
2.9152-2.9830.341340.249718251959100
2.983-3.05760.31131410.24518371978100
3.0576-3.14030.2941410.24317941935100
3.1403-3.23260.2921440.238918431987100
3.2326-3.33690.25161460.220118161962100
3.3369-3.45610.26791470.21618371984100
3.4561-3.59440.24191420.198718341976100
3.5944-3.75790.23931450.187618471992100
3.7579-3.95590.2161460.167118331979100
3.9559-4.20350.18711440.155818572001100
4.2035-4.52770.17971490.15218311980100
4.5277-4.98270.17961440.142518702014100
4.9827-5.7020.19911440.166518752019100
5.702-7.17780.21231510.194719142065100
7.1778-41.22630.23471570.208820002157100

+
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