8SO9 | pdb_00008so9

Phosphoinositide phosphate 3 kinase gamma


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8SO9

This is version 1.3 of the entry. See complete history

Literature

Molecular basis for G beta gamma-mediated activation of phosphoinositide 3-kinase gamma.

Chen, C.L.Syahirah, R.Ravala, S.K.Yen, Y.C.Klose, T.Deng, Q.Tesmer, J.J.G.

(2024) Nat Struct Mol Biol 31: 1198-1207

  • DOI: https://doi.org/10.1038/s41594-024-01265-y
  • Primary Citation Related Structures: 
    8SO9, 8SOA, 8SOB, 8SOC, 8SOD, 8SOE

  • PubMed Abstract: 

    The conversion of phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-triphosphate by phosphoinositide 3-kinase γ (PI3Kγ) is critical for neutrophil chemotaxis and cancer metastasis. PI3Kγ is activated by Gβγ heterodimers released from G protein-coupled receptors responding to extracellular signals. Here we determined cryo-electron microscopy structures of Sus scrofa PI3Kγ-human Gβγ complexes in the presence of substrates/analogs, revealing two Gβγ binding sites: one on the p110γ helical domain and another on the p101 C-terminal domain. Comparison with PI3Kγ alone reveals conformational changes in the kinase domain upon Gβγ binding that are similar to Ras·GTP-induced changes. Assays of variants perturbing the Gβγ binding sites and interdomain contacts altered by Gβγ binding suggest that Gβγ recruits the enzyme to membranes and allosterically regulates activity via both sites. Studies of zebrafish neutrophil migration align with these findings, paving the way for in-depth investigation of Gβγ-mediated activation mechanisms in this enzyme family and drug development for PI3Kγ.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

Macromolecule Content 

  • Total Structure Weight: 226.07 kDa 
  • Atom Count: 12,250 
  • Modeled Residue Count: 1,523 
  • Deposited Residue Count: 1,998 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
phosphatidylinositol-4,5-bisphosphate 3-kinase1,108Sus scrofaMutation(s): 0 
EC: 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt), 2.7.1.153 (UniProt)
UniProt
Find proteins for O02697 (Sus scrofa)
Explore O02697 
Go to UniProtKB:  O02697
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO02697
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 5890Sus scrofaMutation(s): 0 
UniProt
Find proteins for O02696 (Sus scrofa)
Explore O02696 
Go to UniProtKB:  O02696
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO02696
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTCoot9.6
MODEL REFINEMENTPHENIX1.20-4459

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States834497

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2024-09-04
    Changes: Data collection, Database references