9MHG | pdb_00009mhg

Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation

• PDB DOI: https://doi.org/10.2210/pdb9MHG/pdb
• EM Map EMD-48277: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2024-12-11 Released: 2025-02-12 
• Deposition Author(s): Cook, A.S.I., Hurley, J.H., Chen, M.
• Funding Organization(s): Aligning Science Across Parkinsons (ASAP)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structural pathway for class III PI 3-kinase activation by the myristoylated GTPbinding pseudokinase VPS15

Cook, A.S.I., Chen, M., Ngyuen, T.N., Claveras-Cabezudo, A., Khuu, G., Rao, S., Garcia, S.N., Yang, M., Iavarone, A.T., Ren, X., Lazarou, M., Hummer, G., 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 394.36 kDa 
• Atom Count: 22,624 
• Modelled Residue Count: 2,795 
• Deposited Residue Count: 3,464 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase regulatory subunit 4	A	1,409	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R4, VPS15 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 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
Beclin 1-associated autophagy-related key regulator	C	492	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	D	450	Homo sapiens	Mutation(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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-1A	E	226	Homo sapiens	Mutation(s): 1  Gene Names: RAB1A, RAB1 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	F [auth A], I [auth E]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MYR (Subject of Investigation/LOI)	H [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	G [auth A], J [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Cook, A.S.I., Hurley, J.H., Chen, M.

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Funding Organization	Location	Grant Number
Aligning Science Across Parkinsons (ASAP)	United States	ASAP-000350

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release