← Back to search
8emv

Phospholipase C beta 3 (PLCb3) in solution

Method: ELECTRON MICROSCOPY Dmax: 91.2 Å Quality: EXCELLENT
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

Homo sapiens

UniProt Q01970

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 10–1234 Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8EMV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GNK Crystal structure of Galphaq in complex with full-length human PLCbeta3 Deposited 2012-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–1234（1225 aa） Fragment：UNP residues 10-1234
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；277.15 K；100 mM MES pH 6.75, 100-200 mM NaCl, and 11-12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 4.00 Å R-free 0.255
4GNK Crystal structure of Galphaq in complex with full-length human PLCbeta3 Deposited 2012-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 10–1234（1225 aa） Fragment：UNP residues 10-1234
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；277.15 K；100 mM MES pH 6.75, 100-200 mM NaCl, and 11-12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 4.00 Å R-free 0.255
4GNK Crystal structure of Galphaq in complex with full-length human PLCbeta3 Deposited 2012-08-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 934–1192（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；277.15 K；100 mM MES pH 6.75, 100-200 mM NaCl, and 11-12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 4.00 Å R-free 0.255
4QJ3 Structure of a fragment of human phospholipase C-beta3 delta472-559, in complex with Galphaq Deposited 2014-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–470（461 aa） Fragment：UNP residues 10-891
Chain B 570–891（322 aa） Fragment：UNP residues 10-891
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；100 mM BisTris, 200 mM NaCl, 5% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 3.00 Å R-free 0.240
4QJ4 Structure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in complex with Galphaq Deposited 2014-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–470（461 aa） Fragment：UNP residues 10-891
Chain B 570–891（322 aa） Fragment：UNP residues 10-891
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；100 mM BisTris, 200 mM NaCl, 8% (v/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 3.30 Å R-free 0.267
4QJ5 Structure of a fragment of human phospholipase C-beta3 delta472-581, bound to IP3 and in complex with Galphaq Deposited 2014-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–470（461 aa） Fragment：UNP residues 10-891
Chain B 570–891（322 aa） Fragment：UNP residues 10-891
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；277.15 K；100 mM MES, 200 mM NaCl, 5% (v/v) PEG 3350, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 3.41 Å R-free 0.277
7SQ2 Reprocessed and refined structure of Phospholipase C-beta and Gq signaling complex Deposited 2021-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–886（877 aa）
Not recorded ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ACT ACETATE ION × 7 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；7% PEG 6000, 100 mM Hepes, 1 mM CaCl2, 100 mM magnesium acetate
Resolution 2.60 Å R-free 0.263
8EMW Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes Deposited 2022-09-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 10–1234（1225 aa）
Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8EMX Phospholipase C beta 3 (PLCb3) in complex with Gbg on lipid nanodiscs Deposited 2022-09-28 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 9–1234（1226 aa）
Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8UQN PLCb3-Gaq complex on membranes Deposited 2023-10-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–1234（1225 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8UQO PLCb3-Gbg-Gaq complex on membranes Deposited 2023-10-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Q 10–1234（1225 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9Y7H Gb1g2 crosslinked to PLCb3 Deposited 2025-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 10–882（873 aa）
Mutation：E60C, C193S, C221S, C358S, C516S, C824S, C834S ME7 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 100 mM NaCl, 0.1 mM EDTA and 0.1 mM EGTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9YAO Gbg crosslinked to PLCb3 - second conformation Deposited 2025-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 10–882（873 aa）
Mutation：E60C, S193C, S221C, S358C, S824C, S834C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 100 mM NaCl, 0.1 mM EDTA and 0.1 mM EGTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
9YAP Gbg crosslinked to PLCb3 - second conformation Deposited 2025-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 10–882（873 aa）
Mutation：E60C, S193C, S221C, S358C, S824C, S834C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 100 mM NaCl, 0.1 mM EDTA and 0.1 mM EGTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLCB3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–1232； UniProt 10–1234

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8emv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8emv
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8emv
Deposition date deposition_date2022-09-28
Structure title titlePhospholipase C beta 3 (PLCb3) in solution
Keywords keywordsPIP2 degradation, IP3 production, DAG production, G protein signaling, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.40 Å
Radius of gyration Rg (electron density) rg_electron28.33 Å
Forward intensity I(0) i0112391000.00
Molecular weight molecular_weight84556.0 kDa
Excluded volume excluded_volume106470 ų
Envelope volume envelope_volume136470 ų
Hydration-shell volume shell_volume39080 ų
Envelope diameter envelope_diameter96.2 Å
Shell Rg shell_rg36.60 Å
Envelope Rg envelope_rg28.40 Å
Shape Rg shape_rg28.32 Å
Total Rg total_rg29.23 Å
Total atoms total_atoms5949
Residues n_residues747
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax91.2 Å
Rg (real space) rg_real29.29 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real1.1240e+08
I(0) uncertainty (real space) i0_real_error1.6330e+06
Rg (reciprocal space) rg_reciprocal29.34 Å
I(0) (reciprocal space) i0_reciprocal112400000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.5 Å
Skewness Skewness skewness0.219
Kurtosis Kurtosis kurtosis-0.504
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29080000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.958
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8emvA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
▶

8. Citations (1)

▶

9. Files and Curves (10)