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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN VPS34 IN COMPLEX WITH PIK-III
 
Authors :  M. S. Knapp, R. A. Elling
Date :  04 May 14  (Deposition) - 29 Oct 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  B
Keywords :  Vps34, Autophagy, Class Iii, Phosphatidylinositol-3-Kinase, Pik3C3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. E. Dowdle, B. Nyfeler, J. Nagel, R. A. Elling, S. Liu, E. Triantafellow, S. Menon, Z. Wang, A. Honda, G. Pardee, J. Cantwell, C. Luu, I. Cornella-Taracido, E. Harrington, P. Fekkes, H. Lei, Q. Fang, M. E. Digan, D. Burdick, A. F. Powers, S. B. Helliwell, S. D'Aquin, J. Bastien, H. Wang, D. Wiederschain, J. Kuerth, P. Bergman, D. Schwalb, J. Thomas, S. Ugwonali, F. Harbinski, J. Tallarico, C. J. Wilson, V. E. Myer, J. A. Porter, D. E. Bussiere, P. M. Finan, M. A. Labow, X. Mao, L. G. Hamann, B. D. Manning, R. A. Valdez T. Nicholson, M. Schirle, M. S. Knapp, E. P. Keaney, L. O. Murphy
Selective Vps34 Inhibitor Blocks Autophagy And Uncovers A Role For Ncoa4 In Ferritin Degradation And Iron Homeostasis In Vivo.
Nat. Cell Biol. V. 16 1069 2014
PubMed-ID: 25327288  |  Reference-DOI: 10.1038/NCB3053

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3
    Chains: B
    EC Number: 2.7.1.137
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 293-887
    Gene: PIK3C3, VPS34
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTDINS-3-KINASE TYPE 3,PHOSPHATIDYLINOSITOL 3-KINASE P100 SUBUNIT,PHOSPHOINOSITIDE-3-KINASE CLASS 3,HVPS34

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
12UG1Ligand/Ion4'-(CYCLOPROPYLMETHYL)-N~2~-(PYRIDIN-4-YL)-4,5'-BIPYRIMIDINE-2,2'-DIAMINE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:686 , VAL B:688 , THR B:752 , LYS B:753binding site for residue GOL B 901
2AC2SOFTWAREILE B:634 , LYS B:636 , TYR B:670 , MET B:682 , GLN B:683 , PHE B:684 , ILE B:685 , SER B:687 , LEU B:750 , ILE B:760 , ASP B:761 , HOH B:1015 , HOH B:1024 , HOH B:1050binding site for residue 2UG B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PH4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PH4)

(-) Exons   (0, 0)

(no "Exon" information available for 4PH4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain B from PDB  Type:PROTEIN  Length:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...........eee..eeeeeeeee.....ee.......eeeeeee....eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..........eee....eeeee....eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....eee....................hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ph4 B 290 SGIRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF 871
                                   299       309       319       329       339       349       359       369       379       389       399       409       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862         
                                                                                                                                                         417|                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                          471
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PH4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PH4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PH4)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PK3C3_HUMAN | Q8NEB9: 3ihy 3ls8 4oys 4uwf 4uwg 4uwh 4uwk 4uwl 5anl 5enn

(-) Related Entries Specified in the PDB File

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