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- EMDB-25745: CryoEM structure of PLCg1 -

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Basic information

Entry
Database: EMDB / ID: EMD-25745
TitleCryoEM structure of PLCg1
Map data
Sample
  • Complex: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma
  • Ligand: CALCIUM ION
Keywords1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase gamma-1 cryo EM / HYDROLASE
Function / homology
Function and homology information


phosphoinositide phospholipase C / phospholipid catabolic process / phosphatidylinositol phospholipase C activity / intracellular signal transduction / calcium ion binding
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 / Protein kinase C conserved region 2 (CalB) / C2 domain / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsEndo-Streeter S / Sondek J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM057391 United States
CitationJournal: To Be Published
Title: CryoEM structure of PLCg1
Authors: Endo-Streeter S / Sondek J
History
DepositionDec 17, 2021-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25745.png

Downloads & links

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Map

FileDownload / File: emd_25745.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 280 pix.
= 254.8 Å		0.91 Å/pix.
x 280 pix.
= 254.8 Å		0.91 Å/pix.
x 280 pix.
= 254.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.35502547 - 0.66968733
Average (Standard dev.)-0.000033381737 (±0.015356888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 254.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1

EntireName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Components
  • Complex: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma
  • Ligand: CALCIUM ION

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Supramolecule #1: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1

SupramoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma

MacromoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphoinositide phospholipase C
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 138.185391 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AEVLHLCRSL EVGTVMTLFY SKKSQRPERK TFQVKLETRQ ITWSRGADKI EGSIDIREIK EIRPGKTSRD FDRYQEDPAF RPDQSHCFV ILYGMEFRLK TLSLQATSED EVNMWIKGLT WLMEDTLQAA TPLQIERWLR KQFYSVDRNR EDRISAKDLK N MLSQVNYR ...String:
AEVLHLCRSL EVGTVMTLFY SKKSQRPERK TFQVKLETRQ ITWSRGADKI EGSIDIREIK EIRPGKTSRD FDRYQEDPAF RPDQSHCFV ILYGMEFRLK TLSLQATSED EVNMWIKGLT WLMEDTLQAA TPLQIERWLR KQFYSVDRNR EDRISAKDLK N MLSQVNYR VPNMRFLRER LTDLEQRSGD ITYGQFAQLY RSLMYSAQKT MDLPFLETNT LRTGERPELC QVSLSEFQQF LL EYQGELW AVDRLQVQEF MLSFLRDPLR EIEEPYFFLD ELVTFLFSKE NSVWNSQLDA VCPETMNNPL SHYWISSSAN TYL TGDQFS SESSLEAYAR CLRMGCRCIE LDCWDGPDGM PVIYHGHTLT TKIKFSDVLH TIKEHAFVAS EYPVILSIED HCSI AQQRN MAQHFRKVLG DTLLTKPVDI AADGLPSPNQ LKRKILIKHK KLAEGSAYEE VPTSVMYSEN DISNSIKNGI LYLED PVNH EWYPHYFVLT SSKIYYSEET SSDQGNEDEE EPKEASGSTE LHSSEKWFHG KLGAGRDGRH IAERLLTEYC IETGAP DGS FLVRESETFV GDYTLSFWRN GKVQHCRIHS RQDAGTPKFF LTDNLVFDSL YDLITHYQQV PLRCNEFEMR LSEPVPQ TN AHESKEWYHA SLTRAQAEHM LMRVPRDGAF LVRKRNEPNS YAISFRAEGK IKHCRVQQEG QTVMLGNSEF DSLVDLIS Y YEKHPLYRKM KLRYPINEEA LEKIGTAEPD YGALYEGRNP GFYVEANPMP TFKCAVKALF DYKAQREDEL TFTKSAIIQ NVEKQDGGWW RGDYGGKKQL WFPSNYVEEM INPAILEPER EHLDENSPLG DLLRGVLDVP ACQIAIRPEG KNNRLFVFSI SMPSVAQWS LDVAADSQEE LQDWVKKIRE VAQTADARLT EGKMMERRKK IALELSELVV YCRPVPFDEE KIGTERACYR D MSSFPETK AEKYVNKAKG KKFLQYNRLQ LSRIYPKGQR LDSSNYDPLP MWICGSQLVA LNFQTPDKPM QMNQALFMAG GH CGYVLQP STMRDEAFDP FDKSSLRGLE PCVICIEVLG ARHLPKNGRG IVCPFVEIEV AGAEYDSTKQ KTEFVVDNGL NPV WPAKPF HFQISNPEFA FLRFVVYEED MFSDQNFLAQ ATFPVKGLKT GYRAVPLKNN YSEDLELASL LIKIDIFPAK

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMNaClNaCl
10.0 mMMgCl2MgCl2
2.0 mMC4H10O2S2DTT
0.15 mMC24H46O11n-Dodecyl-B-D-Maltoside
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4450 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 13 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 238458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6pbc


Chain - Chain ID: A / Chain - Residue range: 21-1215 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 135.93 / Target criteria: CC fit and model metrics
Output model

PDB-7t8t:
CryoEM structure of PLCg1

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