9ZPD | pdb_00009zpd

Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus

• PDB DOI: https://doi.org/10.2210/pdb9ZPD/pdb
• EM Map EMD-74527: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-12-16 Released: 2025-12-24 
• Deposition Author(s): Chen, M., Ni, Q., Hurley, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Michael J. Fox Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middle Region of C terminus

Chen, M., Ni, Q., Hurley, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 493.97 kDa 
• Atom Count: 17,403 
• Modeled Residue Count: 2,149 
• Deposited Residue Count: 4,357 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase regulatory subunit 4	A	1,445	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R4 EC: 2.7.11.1
UniProt
Find proteins for A0JP11 (Homo sapiens) Explore A0JP11  Go to UniProtKB:  A0JP11

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	B	887	Homo sapiens	Mutation(s): 0  Gene Names: PIK3C3, VPS34 EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens) Explore Q8NEB9  Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9 GTEx:  ENSG00000078142

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UV radiation resistance-associated gene protein	C	699	Homo sapiens	Mutation(s): 0  Gene Names: UVRAG
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2Y5 (Homo sapiens) Explore Q9P2Y5  Go to UniProtKB:  Q9P2Y5
PHAROS:  Q9P2Y5 GTEx:  ENSG00000198382

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera	D, E	663	Homo sapiens	Mutation(s): 0  Gene Names: BECN1, GT197, RUBCN, KIAA0226
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens) Explore Q14457  Go to UniProtKB:  Q14457
PHAROS:  Q14457 GTEx:  ENSG00000126581
Find proteins for Q92622 (Homo sapiens) Explore Q92622  Go to UniProtKB:  Q92622
PHAROS:  Q92622 GTEx:  ENSG00000145016
UniProt Groups	Q14457Q92622

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	F [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN (Subject of Investigation/LOI)	G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.5.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Chen, M., Ni, Q., Hurley, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS134598
Michael J. Fox Foundation	United States	ASAP-000350

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release