9NIE | pdb_00009nie

Cryo-EM structure of the PI3K alpha/KRas/HER3 phosphopeptide complex on POPC/POPS/PIP2 nanodiscs low-pass filtered to 5 angstroms

• PDB DOI: https://doi.org/10.2210/pdb9NIE/pdb
• EM Map EMD-49459: EMDB EMDataResource

• Classification: Transferase/Hydrolase
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-02-26 Released: 2026-05-13 
• Deposition Author(s): Torosyan, H., Natalia, J., Verba, K.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of the PI3K alpha /KRas complex on lipid bilayers reveal molecular mechanisms of PI3K alpha activation.

Torosyan, H., Paul, M.D., Meyer, B.G., Maker, A., Jura, N., Verba, K.A.

(2026) Mol Cell 86: 2858

• PubMed: 42349404 
• DOI: https://doi.org/10.1016/j.molcel.2026.06.010
• Primary Citation Related Structures: 
  9NI3, 9NI4, 9NI5, 9NI6, 9NI7, 9NI8, 9NID, 9NIE, 9NIF, 9NLC


• PubMed Abstract: 
  

  PI3Kα is a potent oncogene that converts PIP2 to PIP3 at the plasma membrane upon activation by receptor tyrosine kinases and Ras. To understand the molecular mechanism of PI3Kα activation, we used cryo-electron microscopy to visualize the conformational states that underlie its transition to an active signaling complex. Here, we present structures of the PI3Kα/KRas complex embedded in lipid nanodiscs, revealing a rich ensemble of PI3Kα conformations that capture the progressive release of key inhibitory domains from the PI3Kα catalytic core. PIP2 triggers significant restructuring of active site regulatory motifs while an activating phosphopeptide induces dimerization of the PI3Kα/KRas complex through a p110α catalytic subunit-mediated interface that is sterically occluded in autoinhibited PI3Kα. In cells, dimeric PI3Kα amplifies Akt signaling in response to growth factor stimulation. Collectively, these structures map the conformational landscape of PI3Kα activation and reveal previously unexplored interfaces for potential therapeutic targeting.

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Organizational Affiliation: 
• Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: [e-mail].
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 150.47 kDa 
• Atom Count: 8,967 
• Modeled Residue Count: 1,091 
• Deposited Residue Count: 1,285 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	1,096	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
GTEx:  ENSG00000121879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	B [auth C]	189	Homo sapiens	Mutation(s): 0  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
GTEx:  ENSG00000133703

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AZD (Subject of Investigation/LOI)	C [auth A]	tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate C29 H32 F N5 O5 S NFCHONNVHGPRMI-UHFFFAOYSA-N
GNP (Subject of Investigation/LOI)	E [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	8.0
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	cryoSPARC	4.3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-13 
Deposition Author(s): Torosyan, H., Natalia, J., Verba, K.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	U54CA274502

Revision History  

• Version 1.0: 2026-05-13
  Type: Initial release
  
• Version 1.1: 2026-07-22
  Changes: Data collection, Database references
• Version 1.2: 2026-07-29
  Changes: Data collection, Database references