9NI7 | pdb_00009ni7

Cryo-EM structure of the Class 3 PI3K alpha/KRas complex on POPC/POPS nanodiscs

PDB DOI: https://doi.org/10.2210/pdb9NI7/pdb
EM Map EMD-49455: EMDB EMDataResource

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

Deposited: 2025-02-25 Released: 2026-05-20
Deposition Author(s): Torosyan, H., Natalia, J., Verba, K.A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NI7

This is version 1.0 of the entry. See complete history.

Literature

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

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

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.03.22.644753

Macromolecule Content

Total Structure Weight: 150.47 kDa
Atom Count: 8,724
Modeled Residue Count: 1,063
Deposited Residue Count: 1,285
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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
PHAROS: P42336 GTEx: ENSG00000121879
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42336
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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) Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AZD (Subject of Investigation/LOI) Query on A1AZD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GNP (Subject of Investigation/LOI) Query on GNP Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.05 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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-05-20
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.