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

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/ncb3053
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3A [auth B]625Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2UG

Download Ideal Coordinates CCD File 
C [auth B]4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine
C17 H17 N7
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
2UG BindingDB:  4PH4 IC50: min: 0.02, max: 18 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 114.532α = 90
b = 114.532β = 90
c = 146.257γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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