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(-) Description

Title :  SORLA VPS10P DOMAIN IN COMPLEX WITH ITS OWN PROPEPTIDE FRAGMENT
 
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 :  3.11
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 - PEPTIDE FROM SORTILIN-RELATED RECEPTOR
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE EXISTS AT THE UPSTREAM OF SORTILIN- RELATED RECEPTOR
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:158 , SER A:160BINDING SITE FOR MONO-SACCHARIDE NAG A 801 BOUND TO ASN A 158
2AC2SOFTWARESER A:366 , ASN A:368 , GLY A:395 , GLY A:396 , SER A:399 , ASP A:400BINDING SITE FOR MONO-SACCHARIDE NAG A 802 BOUND TO ASN A 368
3AC3SOFTWAREASN A:430 , ARG A:439 , PRO A:712 , VAL A:714BINDING SITE FOR MONO-SACCHARIDE NAG A 803 BOUND TO ASN A 430
4AC4SOFTWAREASN A:616 , THR A:618 , ASP A:619BINDING SITE FOR MONO-SACCHARIDE NAG A 804 BOUND TO ASN A 616
5AC5SOFTWAREVAL A:672 , ASN A:674 , THR A:735BINDING SITE FOR MONO-SACCHARIDE NAG A 805 BOUND TO ASN A 674

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:467 -A:473
2A:625 -A:660
3A:643 -A:675
4A:677 -A:736
5A:684 -A:699
6A:716 -A:752

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:156 -Gly A:157
2Asp A:256 -Pro A:257
3Val A:714 -Pro A:715

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WSY)

(-) 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee......eeeeee.......eeeeee..........eeeeee......eee.hhhh...........eeeeee.......eeeee....eeeee.......eeee......eeee.......eeee........eeee......eeeee..eeeeee..........eeeeee.....eeeeee.........eeeeeeeeeeeeee..eeeeeeee.........eeeeeeee.....ee.ee.....eeeeeeeee....eeeeeee....eeeee......eeeeee....ee........hhhhhh....ee.eee.......eeeeee....hhh.eeeeee.......ee...............hhhhh.eeee.hhhhhhhh........ee.......eeeeeeee.......eeeee.......eeee...eeeeee....eeeeee......eeeee.......eeee.....eeeeeee........eeeeeeee.......eeeeeehhhhhh...hhh.eeeehhhhh........eeeeeeee...............eeeee...hhh.eee...eee........eee.............eeee...eee........hhhhhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wsy A  86 QPEPIKVYGQVSLNDSHNQMVVHWAGEKSNVIVALARDSLALARPKSSDVYVSYDYGKSFKKISDKLNFGLGNRSEAVIAQFYHSPADNKRYIFADAYAQYLWITFDFCNTLQGFSIPFRAADLLLHSKASNLLLGFDRSHPNKQLWKSDDFGQTWIMIQEHVKSFSWGIDPYDKPNTIYIERHEPSGYSTVFRSTDFFQSRENQEVILEEVRDFQLRDKYMFATKVVHLLGSEQQSSVQLWVSFGRKPMRAAQFVTRHPINEYYIADASEDQVFVCVSHSNNRTNLYISEAEGLKFSLSLENVLYYSPGGAGSDTLVRYFANEPFADFHRVEGLQGVYIATLINGSMNEENMRSVITFDKGGTWEFLQAPAFTGYGEKINCELSQGCSLHLAQRLSQLLNLQLRRMPILSKESAPGLIIATGSVGKNLASKTNVYISSSAGARWREALPGPHYYTWGDHGGIITAIAQGMETNELKYSTNEGETWKTFIFSEKPVFVYGLLTEPGEKSTVFTIFGSNKENVHSWLILQVNATDALGVPCTENDYKLWSPSDERGNECLLGHKTVFKRRTPHATCFNGEDFDRPVVVSNCSCTREDYECDFGFKMSEDLSLEVCVPDPEFSGPPVPCPSTYRRTRGYRKISGDTCSGGDVEARLEGELVPCP 753
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705 ||    721       731       741       751  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       707|  717|                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        712   720                                 


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ......eeee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3wsy C  42 LPQDRGFLVVQ  52
                                    51
   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 3WSY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
    Leu A:156 - Gly A:157   [ RasMol ]  
    Val A:714 - Pro A:715   [ RasMol ]  
 

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  3wsy
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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 3wsz

(-) Related Entries Specified in the PDB File

3wsx SAME PROTEIN LIGAND-FREE FORM
3wsz SAME PROTEIN COMPLEX WITH ABETA-DERIVED PEPTIDE