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(-) Description

Title :  NEGATIVE STAIN STRUCTURE OF VPS15/VPS34 COMPLEX
 
Authors :  M. L. Kirsten, L. Zhang, Y. Ohashi, O. Perisic, R. L. Williams, C. Sachse
Date :  04 Jun 16  (Deposition) - 05 Oct 16  (Release) - 09 Nov 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  28.00
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Autophagy, Phosphatidylinositol 3-Kinase (Ptdins3K), Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Ohashi, N. Soler, M. Garcia Ortegon, L. Zhang, M. L. Kirsten, O. Perisic, G. R. Masson, J. E. Burke, A. J. Jakobi, A. A. Apostolakis, C. M. Johnson, M. Ohashi, N. T. Ktistakis, C. Sachse, R. L. Williams
Characterization Of Atg38 And Nrbf2, A Fifth Subunit Of The Autophagic Vps34/Pik3C3 Complex.
Autophagy V. 12 2129 2016
PubMed-ID: 27630019  |  Reference-DOI: 10.1080/15548627.2016.1226736

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE VPS34
    Chains: C
    EC Number: 2.7.1.137
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Gene: VPS34, END12, PEP15, VPL7, VPT29, YLR240W, L9672.10
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PTDINS-3-KINASE VPS34,CARBOXYPEPTIDASE Y-DEFICIENT PROTEIN 15,VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 34,VACUOLAR PROTEIN- TARGETING PROTEIN 29
 
Molecule 2 - SERINE/THREONINE-PROTEIN KINASE VPS15
    Chains: B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Gene: VPS15, GRD8, VAC4, VPL19, YBR097W, YBR0825
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: GOLGI-RETENTION DEFECTIVE MUTANT PROTEIN 8,VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 15

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5KC2)

(-) Sites  (0, 0)

(no "Site" information available for 5KC2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KC2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KC2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KC2)

(-) Exons   (0, 0)

(no "Exon" information available for 5KC2)

(-) 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:1224
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................ee.......eeee.........eee.....hhhhh..hhhhhhhhhhhhhh......eeee........eee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.................................hhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.............hhhhhhhhh.....hhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhh....hhhhh..hhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh...............hhhhhhhhh......hhhhhhh..................eeeeee..........eeee.....eeee.....eeeeeehhhhhh.......eeee....eeeeee......eeeee...eeeeeeeeeeee..eeeeeeeeeeeeee.hhhh.......eeeee....eeeeee....eeeeee....eeeeeee.hhhhh.....ee.....eeeee.....eeeee....eeeeee.........eee........eeeee.....eeeeeee....eeeeeeee.....hhhhhh......................eeee..eeeeee....eeeeee.......eeee.......eeeeeeee..eeeeeee.........eeeeeeee....eeeeeee....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kc2 B   10 QASPSIAIFSYIDVLEEVHYVSQLNSSRFLKTCKALDPNGEIVIKVFIKPKDQYSLRPFLQRIRAQSFKLGQLPHVLNYSKLIETNRAGYMIRQHLKNNLYDRLSLRPYLQDIELKFIAFQLLNALKDIHNLNIVHGDIKTENILVTSWNWCILTDFAAFTCYLAPERFNSKLYQDGKSNNGRLTKEMDIFSLGCVIAEIFAEGRPIFNLSQLFKYKSNSYDVNRSTDLRNLVLDMIQLDPSKRLSCDELLNKYRGIFFPDYFYTFIYDYFRNLVTMTNTCTNSTLEDNVKLLDETTEKIYRDFSQICHCLDFPLIKDGGEIGSDPPILLVLQQFTKVSEKIKSVKEECALLFISYLSHSIRSIVSTATKLKNLELLAVFAQFVSDENKIDRVVPYFVCCFEDSDQDVQALSLLTLIQVLTSVRKLNQLNENIFVDYLLPRLKRLLISNRQNTNYLRIVFANCLSDLAIIINRFQEFTFAQHCNDNSSTKYSAKLIQSVEDLTVSFLTDNDTYVKMALLQNRERTNDIILSHLITYLNDKDPALRVSLIQTISGISILLGTVTLEQYILPLLIQTITDSEELVVISVLQSLKSLFKTGLIRKKYYIDISKTTSPLLLHPNNWIRQFTLMIIIEIINKLSKAEVYCILYPIIVEFNFKSMISCCKQPVSRSVYNLLCSWSVRASKSLFWKKIITNHVDSFGNNRIEFITKSTVYSHDNKEIPLTAEDRNWIDKFHIIGLTEKDIWKIVALRGYVIRTARVMAANPNLKNVFVQLEPTSYHMHSPNHGLKDNANVKPERKVVVSNSYEGDVESIEKFLSTFKILPPLRDYKEFGPIQEIVRSPNMGNLRGKLIATLMENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEIIVGEVYSSSLTYDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNHYQQESEVKFLNCECIRKINLKNFGKNEYAVRMRAFVNEEKSLLVALTNLSRVIIFDIRTLERLQIIENSPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSFGDHAPITHVEVCQFYGKNSVIVVGGSSKTFLTIWNFVKGHCQYAFINSDEQPSMEHFLPIEKGLEELNFCGIRSLNALSTISVSNDKILLTDEATSSIVMFSLNELSSSKAVISPSRFSDVFIPTQVTANLTMLLRKMKSLYHHDIINSISTCEVDETPLLVACDNSGLIGIFQ 1454
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169|      203       213       223       233       243       253    || 271       281       291       301       311       328       338       348       358       368       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552      |572       582       592       602||     621       631       641       651       661       671       681       691       701       711       721       731       741||     758       768       778       788       798       834       844       854       864       874       884   ||  991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1420      1430      1440      1450    
                                                                                                                                                                                         169|                                                             258|                                                 319|                                               377|                                                                                                                                                          559|                              603|                                                                                                                              742|                                                      807|                                                   888|                                                                                                                                                                                                                                                                                                                                                                                                                                    1410|                                  
                                                                                                                                                                                          194                                                              267                                                  327                                                402                                                                                                                                                           570                               613                                                                                                                               750                                                       834                                                    986                                                                                                                                                                                                                                                                                                                                                                                                                                     1420                                  


Chain C from PDB  Type:PROTEIN  Length:783
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee....................hhhhhhh.........ee..ee....ee....ee.............eeeeeeee........eeeeee...........eeeeee......hhhhh.eeeeeee........hhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh......eeeeeee.....................hhhhhhhhhhhh.............hhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhh.......hhhhh.......hhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..ee.......ee...eeeeeee.......eeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhh...........ee......eeee....eehhhhhhh..hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........eeee...eeee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kc2 C    4 NNITFCVSQDLDVPLKVKIKSLEGHKPLLKPSQKILNPELMLIGSNVFPSSDLIVSLQVFDKERNRNLTLPIYTPYIPFRNSRTWDYWLTLPIRIKQLTFSSHLRIILWEYNGSKQIPFFNLETSIFNLKDCTLKRGFESLKFRYDVIDHCEVVTDNKDQENLNKYFQGEFTRLPWLDEITISKLRKQRENRTWPQGTFVLNLEFPMLELPVVFIEREIMNTNDPIEEKYRRLERASKNANLDKQVKPDIKKRDYLNKIINYPPGTKLTAHEKGSIWKYRYYLMNNKKALTKLLQSTNLREESERVEVLELMDSWAEIDIDDALELLGSTFKNLSVRSYAVNRLKKASDKELELYLLQLVEAVCFENLSTFSDKSNSEFTIVDAVSPLAEFLIRRALVNPRLGSFFYWYLKSESEDKPYLDQILSSFWSRLDKKSRNILNDQVRLINVLRECCETIKRLKDTTAKKMELLVHLLETKVRPLVKVRPIALPLDPDVLICDVCPETSKVFKSSLSPLKITFKTTLNQPYHLMFKVGDDLRQDQLVVQIISLMNELLKNENVDLKLTPYKILATGPQEGAIEFIPNDTLASILSKYHGILGYLKLHYPDENATLGVQGWVLDNFVKSCAGYCVITYILGVGDRHLDNLLVTPDGHFFHADFGYILGQDPKPFPPLMKLPPQIIEAFGGAESSNYDKFRSYCFVAYSILRRNAGLILNLFELMKTSNIPDIRIDPNGAILRVRERFNLNMSEEDATVHFQNLINDSVNALLPIVIDHLHNLAQYWRT  875
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 ||    281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431     ||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       872   
                                                                                                                                                                                                                                                       225|                                                                                                                                                                437|                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                        274                                                                                                                                                                 479
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 5KC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KC2)

(-) Gene Ontology  (37, 58)

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  5kc2
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  VPS15_YEAST | P22219
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  VPS34_YEAST | P22543
    Comparative Protein Structure Models: ModBase
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  2.7.1.137
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS15_YEAST | P22219: 3gre 5dfz
        VPS34_YEAST | P22543: 5dfz

(-) Related Entries Specified in the PDB File

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