8SOB

Phosphoinositide phosphate 3 kinase gamma bound with ADP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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:  (by identity cutoff)  |  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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot9.6
MODEL REFINEMENTPHENIX1.20-4459
RECONSTRUCTIONcryoSPARC3.3.1

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