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(-) Description

Title :  SORLA VPS10P DOMAIN IN COMPLEX WITH ABETA-DERIVED PEPTIDE
 
Authors :  Y. Kitago, Z. Nakata, M. Nagae, T. Nogi, J. Takagi
Date :  30 Mar 14  (Deposition) - 04 Feb 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Beta-Propeller, Receptor, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kitago, M. Nagae, Z. Nakata, M. Yagi-Utsumi, S. Takagi-Niidome, E. Mihara, T. Nogi, K. Kato, J. Takagi
Structural Basis For Amyloidogenic Peptide Recognition By Sorla
Nat. Struct. Mol. Biol. 2015
PubMed: search  |  Reference-DOI: 10.1038/NSMB.2954

(-) Compounds

Molecule 1 - SORTILIN-RELATED RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO CELLS
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PEF
    Expression System Taxid: 10029
    Expression System Variant: LEC 3.2.8.1
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 86-753
    Gene: SORL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURONAL EXTRACELLULAR RECEPTOR
 
Molecule 2 - 10-MER PEPTIDE
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:158 , SER A:160 , PRO A:227 , ASN A:228BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 158
2AC2SOFTWAREASN A:430BINDING SITE FOR MONO-SACCHARIDE NAG A 802 BOUND TO ASN A 430
3AC3SOFTWARETYR A:93 , ASN A:616 , THR A:618 , ASP A:619BINDING SITE FOR MONO-SACCHARIDE NAG A 803 BOUND TO ASN A 616
4AC4SOFTWAREASN A:674BINDING SITE FOR MONO-SACCHARIDE NAG A 804 BOUND TO ASN A 674

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:467 -A:473
2A:625 -A:660
3A:643 -A:675

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:256 -Pro A:257
2Gly A:395 -Gly A:396
3Glu A:605 -Asn A:606
4Gly A:640 -Asn A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WSZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WSZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3WSZ)

(-) 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:561
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeee.......eeeeee.......eeeee.......ee.hhhh...........eeeeee.......eeeee....eeeee.......eeee......eeee.......eeee........eeee.......eeee..eeeeee..........eeeeee.....eeeeee..........ee......eeeee..eeeee.........eeee..eeeee........eeeeeeeeee..eeeeeeee....eeeee....eeeee...ee........hhhhhh....ee.eee.......eeeeee...eeeeee.......ee..................eeeeehhhhhhhh........ee.......eeeeeeee.......eeeee.......eeee...eeeeee....eeeeee......eeeee.......eeee......eeeeee........eeeeeee.......eeeeeeehhhhhh...hhh.eeeehhhhhh.....eeeeee...............eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsz A  88 EPIKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLPKSSDVYVSYDYGKSFKKISDKLNFGLGNRSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLLLHSKASNLLLGFDRSHPNKQLWKSDDFGQTWIMIQEHVKSFSWGIDPYDKPNTIYIERHEPSGYSTVFRSTDFFQSRENQEVILEEVRDFQLRDKYMFATKVVHLLGSLWVSFGRKPMRAAQFVTRHPINEYYIADASEDQVFVCVSHSNNRTNLYISEKFSLSLENVLYYSPGGAGSDTLVRYFANEPFADFHRVEGLQGVYIATLINGNMRSVITFDKGGTWEFLQAPAFTGKINCELSQGCSLHLAQRLSQLLNLQLRRMPILSKESAPGLIIATGSVGKNLASKTNVYISSSAGARWREALPGPHYYTWGDHGGIITAIAQGMETNELKYSTNEGETWKTFIFSEKPVFVYGLLTEPGEKSTVFTIFGSNKENVHSWLILQVNATDALGVPCTENDYKLWSPSDERGNECKTVFKRRTPHATCFNGEDFDRPVVVSNC 675
                                    97       107       117       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      |328       338       348       358       368       382       392       402       412       422       437       447       457  ||   470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640  ||   654       664       674 
                                                               125|                                                                                                                                                                                         318|                                               376|                                               431|                    460|                                                                                                                                                                                643|                           
                                                                130                                                                                                                                                                                          326                                                381                                                437                     464                                                                                                                                                                                 648                           


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ...ee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3wsz C   9 AAAAAAA  15
   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 3WSZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WSZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WSZ)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:256 - Pro A:257   [ RasMol ]  
    Glu A:605 - Asn A:606   [ RasMol ]  
    Gly A:395 - Gly A:396   [ RasMol ]  
    Gly A:640 - Asn A:641   [ RasMol ]  
 

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  3wsz
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  SORL_HUMAN | Q92673
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 Related Entries

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

UniProtKB/Swiss-Prot
        SORL_HUMAN | Q92673: 2dm4 3g2s 3g2t 3wsx 3wsy

(-) Related Entries Specified in the PDB File

3wsx SAME PROTEIN LIGAND-FREE FORM
3wsy SAME PROTEIN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT