9ZPC | pdb_00009zpc

Cryo-EM structure of human PI3KC3-C2

  • 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., Joiner, A., Hurley, J.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Michael J. Fox Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


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


Literature

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

Chen, M., Joiner, A., Hurley, J.H.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 41,445Homo sapiensMutation(s): 0 
Gene Names: PIK3R4
EC: 2.7.11.1
UniProt
Find proteins for A0JP11 (Homo sapiens)
Explore A0JP11 
Go to UniProtKB:  A0JP11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0JP11
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3887Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UV radiation resistance-associated gene protein699Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2Y5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin-1450Homo sapiensMutation(s): 0 
Gene Names: BECN1, GT197
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens)
Explore Q14457 
Go to UniProtKB:  Q14457
PHAROS:  Q14457
GTEx:  ENSG00000126581 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14457
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5.3
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS134598
Michael J. Fox FoundationUnited StatesASAP-000350

Revision History  (Full details and data files)

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