7MEZ | pdb_00007mez

Structure of the phosphoinositide 3-kinase p110 gamma (PIK3CG) p101 (PIK3R5) complex

• PDB DOI: https://doi.org/10.2210/pdb7MEZ/pdb
• EM Map EMD-23808: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Sus scrofa
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2021-04-08 Released: 2021-07-14 
• Deposition Author(s): Burke, J.E., Dalwadi, U., Rathinaswamy, M.K., Yip, C.K.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the phosphoinositide 3-kinase (PI3K) p110 gamma-p101 complex reveals molecular mechanism of GPCR activation.

Rathinaswamy, M.K., Dalwadi, U., Fleming, K.D., Adams, C., Stariha, J.T.B., Pardon, E., Baek, M., Vadas, O., DiMaio, F., Steyaert, J., Hansen, S.D., Yip, C.K., Burke, J.E.

(2021) Sci Adv 7

• PubMed: 34452907 
• DOI: https://doi.org/10.1126/sciadv.abj4282
• Primary Citation Related Structures: 
  7MEZ


• PubMed Abstract: 
  

  The class IB phosphoinositide 3-kinase (PI3K), PI3Kγ, is a master regulator of immune cell function and a promising drug target for both cancer and inflammatory diseases. Critical to PI3Kγ function is the association of the p110γ catalytic subunit to either a p101 or p84 regulatory subunit, which mediates activation by G protein-coupled receptors. Here, we report the cryo-electron microscopy structure of a heterodimeric PI3Kγ complex, p110γ-p101. This structure reveals a unique assembly of catalytic and regulatory subunits that is distinct from other class I PI3K complexes. p101 mediates activation through its Gβγ-binding domain, recruiting the heterodimer to the membrane and allowing for engagement of a secondary Gβγ-binding site in p110γ. Mutations at the p110γ-p101 and p110γ-adaptor binding domain interfaces enhanced Gβγ activation. A nanobody that specifically binds to the p101-Gβγ interface blocks activation, providing a novel tool to study and target p110γ-p101-specific signaling events in vivo.

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Organizational Affiliation: 
• Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.
Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada. [e-mail] [e-mail].
Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 224.1 kDa 
• Atom Count: 12,361 
• Modeled Residue Count: 1,536 
• Deposited Residue Count: 1,983 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	1,102	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.1.154 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase regulatory subunit 5	B	881	Sus scrofa	Mutation(s): 2  Gene Names: PIK3R5
UniProt
Find proteins for O02696 (Sus scrofa) Explore O02696  Go to UniProtKB:  O02696

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Burke, J.E., Dalwadi, U., Rathinaswamy, M.K., Yip, C.K.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	168998

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2022-04-06
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Data collection
• Version 1.3: 2025-05-14
  Changes: Data collection, Structure summary