4PH4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1038/ncb3053

  • 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 b ...

    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.,Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.,Novartis Institutes for BioMedical Research, 4560 Horton Street Emeryville, California 94608, USA.,Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase catalytic subunit type 3
B
625Homo sapiensMutation(s): 0 
Gene Names: PIK3C3 (VPS34)
EC: 2.7.1.137
Find proteins for Q8NEB9 (Homo sapiens)
Go to Gene View: PIK3C3
Go to UniProtKB:  Q8NEB9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2UG
Query on 2UG

Download SDF File 
Download CCD File 
B
4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine
C17 H17 N7
XXSDLQLNIVFIJI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.532α = 90.00
b = 114.532β = 90.00
c = 146.257γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER-TNTrefinement
BUSTERrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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