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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GAMMA-SECRETASE COMPONENT NICASTRIN
 
Authors :  T. Xie, C. Yan, R. Zhou, Y. Zhao, L. Sun, G. Yang, P. Lu, D. Ma, Y. Shi
Date :  03 Aug 14  (Deposition) - 17 Sep 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta, Nicastrin, Putative Substrate-Recruiting Component, Gamma-Secretase Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Xie, C. Yan, R. Zhou, Y. Zhao, L. Sun, G. Yang, P. Lu, D. Ma, Y. Shi
Crystal Structure Of The Gamma-Secretase Component Nicastri
Proc. Natl. Acad. Sci. Usa 2014
PubMed-ID: 25197054  |  Reference-DOI: 10.1073/PNAS.1414837111

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 19-611
    Gene: DICPUDRAFT_96800
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM PURPUREUM
    Organism Taxid: 5786
    Synonym: NICASTRIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:543 , CYS A:546 , SER A:549 , HOH A:1177 , HOH A:1213 , HOH A:1225BINDING SITE FOR RESIDUE CA A 809
2AC2SOFTWAREASP A:71 , ASN A:93 , TYR A:94 , ASN A:96 , TYR A:122 , HOH A:1246BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 96 RESIDUES 803 TO 805
3AC3SOFTWARETHR A:116 , ASP A:117 , THR A:118 , LYS A:119 , ASN A:166BINDING SITE FOR MONO-SACCHARIDE NAG A 806 BOUND TO ASN A 166
4AC4SOFTWAREASN A:333 , THR A:335 , LYS A:336BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 333 RESIDUES 801 TO 802
5AC5SOFTWAREGLY A:59 , GLY A:60 , SER A:62 , GLU A:384 , ASN A:385BINDING SITE FOR MONO-SACCHARIDE NAG A 807 BOUND TO ASN A 385
6AC6SOFTWAREASN A:584 , TYR A:587BINDING SITE FOR MONO-SACCHARIDE NAG A 808 BOUND TO ASN A 584

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:54
2A:204 -A:210
3A:308 -A:318
4A:479 -A:486
5A:540 -A:551
6A:546 -A:556

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:320 -Pro A:321

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R12)

(-) Exons   (0, 0)

(no "Exon" information available for 4R12)

(-) 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 A from PDB  Type:PROTEIN  Length:573
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeee...eeee......eeeeeeee.hhhhhhh........eeeeee.hhhhhhhhhhh.....eeeeeee.................hhhhh..............hhhh.ee...eeeehhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhh.eee..eeeeeee..........eeeeeee......hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh...ee......eee.....hhhhhhhhhh.eeeeeee......eee....eeeeeeeee...hhhhhhhhhhhhh......eeeee.........hhhhhhh......eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhh................eee..ee..hhhhhhhhhhhhhhh..eeee....hhhhh...eee..eeee.eeeeeee....eeee....eeee.......eeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r12 A  33 YTTLYSSYPCTKIMTSDGQFGCSSKHGGNSGILYLIDDDESYNNYFSYSQQKDIIVVLDTNYFNSTSVLNLHNKSKIEGIIVLTDTKKTYPYSPDSRYPNKIYGLYPNSNLEWNPNADGFTYFSFPFPIFAIDNQTSVAIRNVSKHNRDGQYPAWGAELDSFMQGAINSETCLRRGFCEPVGGQSIWSSFSSKIDKEKEIILVMLPFDTTAFFRDLSIGADQSSFATVTLLSVIKSLAAVDRSSWNKEVVFAFWNAERWGYVGSEYFINDLLNFQCKTYNSDKSKCIDPPRADLAFQTQINFTKISTIIELNQIGRAQLDKNLGKYSLYLHTAGTKTSSVTDILDQVASSYENSTITFKPTTQTELPPSSSMSFLKKTNKIPVVVITDHDYKYSNPYYGYEQDDNENVLGSTLNDIVYILSTFIDRIAGGNNNITIDKNFINILYPCFTSSITCFNILMKTYPLNEVPNFYSSVFGTSLTTTLSPYETKLIHRLLYSITQYNSTLTNCTSDNDCPSSLCYSGQCVSSNTHLHNALSLGFDFDTSKNVWKIVNSSYPIFTESNWDYTALKVFKI 605
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602
   Legend:   → Mismatch (orange background)
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  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 4R12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R12)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asp A:320 - Pro A:321   [ RasMol ]  
 

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