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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SNX27 PDZ DOMAIN BOUND TO THE C-TERMINAL DGKZETA PDZ BINDING MOTIF
 
Authors :  B. M. Collins, T. Clairfeuille
Date :  05 Nov 15  (Deposition) - 07 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A,B,C,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,C  (1x)
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, B
    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 - GLU-ASP-GLN-GLU-THR-ALA-VAL
    Chains: P, C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCP
Biological Unit 1 (1x): A  P
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PG44Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:110 , ALA A:112 , GLN A:116 , HOH A:304 , HOH A:321 , HOH A:323 , HOH A:360 , VAL B:61 , PG4 B:201 , HOH B:392binding site for residue PG4 A 201
2AC2SOFTWAREGLN A:66 , PG4 A:201 , GLU B:63 , ASN B:108 , GLU B:110 , GLY B:111 , ALA B:112 , GLN B:116 , HOH B:384binding site for residue PG4 B 201
3AC3SOFTWARELEU A:85 , HOH A:374 , ASN B:105 , GLU B:127 , HOH P:309binding site for residue PG4 B 202
4AC4SOFTWAREHOH C:417binding site for residue PG4 C 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ELQ)

(-) Sequences/Alignments

Asymmetric 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:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeeee.......eee..eee....eeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5elq A  41 PRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAGVRKGDRILEVNGVNVEGATHKQVVDLIRAGEKELILTVLS 134
                                    50        60        70        80        90       100       110       120       130    


Chain B from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee.......eee..eee....eeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5elq B  40 SPRVVRIVKSESGYGFNVRGQVSEGGQLRSINGELYAPLQHVSAVLPGGAADRAGVRKGDRILEVNGVNVEGATHKQVVDLIRAGEKELILTVLS 134
                                    49        59        69        79        89        99       109       119       129     


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeeee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5elq C 201 EDQETAV 207


Chain P from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeeee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5elq P 201 EDQETAV 207
   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 5ELQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 44)

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  DGKZ_HUMAN | Q13574
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  SNX27_RAT | Q8K4V4
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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 5em9 5ema 5emb

(-) Related Entries Specified in the PDB File

4z8j SNX27 PDZ DOMAIN BOUND TO RELATED PDZ PEPTIDE MOTIF
5em9
5ema
5emb