4PH4

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


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 

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Ligand Structure Quality Assessment 


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
  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3A [auth B]625Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEB9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2UG
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
XXSDLQLNIVFIJI-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 114.532α = 90
b = 114.532β = 90
c = 146.257γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHASERphasing
BUSTERrefinement
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