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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SNX27 PDZ DOMAIN BOUND TO THE PHOSPHORYLATED C-TERMINAL LRRC3B PDZ BINDING MOTIF
 
Authors :  B. M. Collins, T. Clairfeuille
Date :  06 Nov 15  (Deposition) - 07 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endosome, Pdz Domain, Sorting Nexin, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Clairfeuille, C. Mas, A. S. Chan, Z. Yang, M. Tello-Lafoz, M. Chandra, J. Widagdo, M. C. Kerr, B. Paul, I. Merida, R. D. Teasdale, N. J. Pavlos, V. Anggono, B. M. Collins
A Molecular Code For Endosomal Recycling Of Phosphorylated Cargos By The Snx27-Retromer Complex.
Nat. Struct. Mol. Biol. V. 23 921 2016
PubMed-ID: 27595347  |  Reference-DOI: 10.1038/NSMB.3290

(-) Compounds

Molecule 1 - SORTING NEXIN-27
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PDZ DOMAIN (UNP RESIDUES 39-133)
    Gene: SNX27, MRT1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: MAP-RESPONSIVE GENE PROTEIN,METHAMPHETAMINE-RESPONSIVE TRANSCRIPT 1 PROTEIN,PDZ-PROTEIN MRT1
 
Molecule 2 - ASP-ASP-ILE-SEP-THR-VAL-VAL
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:56 , LEU A:74 , ALA A:83 , ASN A:105 , GLU A:127 , HOH A:310 , HOH A:313binding site for residue GOL A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMA)

(-) 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:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......eeeee........eee..eee....eeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5ema A  40 SPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAGVRKGDRILEVNGVNVEGATHKQVVDLIRAGEKELILTVLSV 135
                                    49        59        69        79        89        99       109       119       129      


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               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
                 5ema B   1 DDIsTVV   7
                               |   
                               4-SEP
   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 5EMA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 23)

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
        SNX27_RAT | Q8K4V4: 3qdo 3qe1 3qgl 4p2a 4z8j 5elq 5em9 5emb

(-) Related Entries Specified in the PDB File

4z8j 5elq 5em9 5emb