Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.26 kDa 
• Atom Count: 4367 
• Modelled Residue Count: 529 
• Deposited Residue Count: 625 
• Unique protein chains: 1

4PH4

The crystal structure of Human VPS34 in complex with PIK-III

• PDB DOI: 10.2210/pdb4PH4/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-05-04 Released: 2014-10-29 
• Deposition Author(s): Knapp, M.S., Elling, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo.

Dowdle, W.E., Nyfeler, B., Nagel, J., Elling, R.A., Liu, S., Triantafellow, E., Menon, S., Wang, Z., Honda, A., Pardee, G., Cantwell, J., Luu, C., Cornella-Taracido, I., Harrington, E., Fekkes, P., Lei, H., Fang, Q., Digan, M.E., Burdick, D., Powers, A.F., Helliwell, S.B., D'Aquin, S., Bastien, J., Wang, H., Wiederschain, D., Kuerth, J., Bergman, P., Schwalb, D., Thomas, J., Ugwonali, S., Harbinski, F., Tallarico, J., Wilson, C.J., Myer, V.E., Porter, J.A., Bussiere, D.E., Finan, P.M., Labow, M.A., Mao, X., Hamann, L.G., Manning, B.D., Valdez, R.A., Nicholson, T., Schirle, M., Knapp, M.S., Keaney, E.P., Murphy, L.O.

(2014) Nat Cell Biol 16: 1069-1079

• PubMed: 25327288 
• DOI: 10.1038/ncb3053
• Primary Citation of Related Structures:  
  4PH4


• PubMed Abstract: 
  

Cells rely on autophagy to clear misfolded proteins and damaged organelles to maintain cellular homeostasis. In this study we use the new autophagy inhibitor PIK-III to screen for autophagy substrates. PIK-III is a selective inhibitor of VPS34 that binds a unique hydrophobic pocket not present in related kinases such as PI(3)Kα. PIK-III acutely inhibits autophagy and de novo lipidation of LC3, and leads to the stabilization of autophagy substrates. By performing ubiquitin-affinity proteomics on PIK-III-treated cells we identified substrates including NCOA4, which accumulates in ATG7-deficient cells and co-localizes with autolysosomes. NCOA4 directly binds ferritin heavy chain-1 (FTH1) to target the iron-binding ferritin complex with a relative molecular mass of 450,000 to autolysosomes following starvation or iron depletion. Interestingly, Ncoa4(-/-) mice exhibit a profound accumulation of iron in splenic macrophages, which are critical for the reutilization of iron from engulfed red blood cells. Taken together, the results of this study provide a new mechanism for selective autophagy of ferritin and reveal a previously unappreciated role for autophagy and NCOA4 in the control of iron homeostasis in vivo.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	A [auth B]	625	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2UG	C [auth B]	4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine C17 H17 N7 XXSDLQLNIVFIJI-UHFFFAOYSA-N
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2UG	BindingDB:  4PH4	IC50: min: 0.02, max: 18 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.532	α = 90
b = 114.532	β = 90
c = 146.257	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
BUSTER	refinement
XSCALE	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-04 
• Released Date: 2014-10-29 
Deposition Author(s): Knapp, M.S., Elling, R.A.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references
• Version 1.2: 2014-11-12
  Changes: Database references
• Version 1.3: 2015-02-04
  Changes: Derived calculations