9MHF | pdb_00009mhf

Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


This is version 1.1 of the entry. See complete history


Literature

Structural pathway for PI3-kinase regulation by VPS15 in autophagy.

Cook, A.S.I.Chen, M.Nguyen, T.N.Cabezudo, A.C.Khuu, G.Rao, S.Garcia, S.N.Yang, M.Iavarone, A.T.Ren, X.Lazarou, M.Hummer, G.Hurley, J.H.

(2025) Science 388: eadl3787-eadl3787

  • DOI: https://doi.org/10.1126/science.adl3787
  • Primary Citation of Related Structures:  
    9MHF, 9MHG, 9MHH

  • PubMed Abstract: 

    The class III phosphatidylinositol-3 kinase complexes I and II (PI3KC3-C1 and PI3KC3-C2) have vital roles in macroautophagy and endosomal maturation, respectively. We elucidated a structural pathway of enzyme activation through cryo-electron microscopy analysis of PI3KC3-C1. The inactive conformation of the VPS15 pseudokinase stabilizes the inactive conformation, sequestering its N -myristate in the N-lobe of the pseudokinase. Upon activation, the myristate is liberated such that the VPS34 lipid kinase catalyzes phosphatidylinositol-3 phosphate production on membranes. The VPS15 pseudokinase domain binds tightly to guanosine triphosphate and stabilizes a web of interactions to autoinhibit the cytosolic complex and promote activation upon membrane binding. These findings show in atomistic detail how the VPS34 lipid kinase is activated in the context of a complete PI3K complex.


  • Organizational Affiliation
    • Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 41,409Homo sapiensMutation(s): 0 
Gene Names: PIK3R4VPS15
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99570 (Homo sapiens)
Explore Q99570 
Go to UniProtKB:  Q99570
PHAROS:  Q99570
GTEx:  ENSG00000196455 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99570
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3887Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin 1-associated autophagy-related key regulator492Homo sapiensMutation(s): 0 
Gene Names: ATG14
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZNE5 (Homo sapiens)
Explore Q6ZNE5 
Go to UniProtKB:  Q6ZNE5
PHAROS:  Q6ZNE5
GTEx:  ENSG00000126775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZNE5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin-1450Homo sapiensMutation(s): 0 
Gene Names: BECN1GT197
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens)
Explore Q14457 
Go to UniProtKB:  Q14457
PHAROS:  Q14457
GTEx:  ENSG00000126581 
Entity Groups  
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UniProt GroupQ14457
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-1A226Homo sapiensMutation(s): 1 
Gene Names: RAB1ARAB1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62820 (Homo sapiens)
Explore P62820 
Go to UniProtKB:  P62820
PHAROS:  P62820
GTEx:  ENSG00000138069 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62820
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Aligning Science Across Parkinsons (ASAP)United StatesASAP-000350

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references