9ZPD | pdb_00009zpd

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

  • 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

Experimental Data Snapshot

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

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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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., Ni, Q., Hurley, J.H.

To be published.

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

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|  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
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UniProt GroupA0JP11
Sequence Annotations
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Reference Sequence
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|  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 
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UniProt GroupQ8NEB9
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Reference Sequence
Find similar proteins by:
|  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 
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UniProt GroupQ9P2Y5
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera
D, E
663Homo sapiensMutation(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 
Entity Groups
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UniProt GroupsQ14457Q92622
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.5.3

Structure Validation

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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