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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOX HOMOLOGY DOMAIN OF HUMAN SORTING NEXIN 24
 
Authors :  A. E. Oberholzer, W. Kiyani, T. Krojer, L. Shrestha, F. Von Delft, D. S. A. Chaikuad, J. Raynor, C. Arrowsmith, A. Edwards, C. Bountra, W. W. Yu
Date :  24 Jun 12  (Deposition) - 10 Oct 12  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. E. Oberholzer, W. Kiyani, T. Krojer, L. Shrestha, F. Von Delft, D. S. Froese, A. Chaikuad, J. Raynor, C. Arrowsmith, A. Edwards, C. Bountra, W. W. Yue
Crystal Structure Of Phox Homology Domain Of Human Sorting Nexin 24
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SORTING NEXIN-24
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentPHOX HOMOLOGY DOMAIN, RESIDUES 160-266
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A (1x)B (1x)
Biological Unit 2 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:66 , PRO A:68 , HOH A:2116 , TYR B:10 , TRP B:66 , PRO B:68 , LEU B:71BINDING SITE FOR RESIDUE EDO A1103
2AC2SOFTWARELYS A:48 , LYS A:51 , LEU A:95 , LYS B:48 , LYS B:51 , LEU B:95BINDING SITE FOR RESIDUE EDO A1104

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:52 -B:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AZ9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX24_HUMAN1-125
 
  2A:1-102
B:1-105
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX24_HUMAN1-125
 
  2A:1-102
B:1-105
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX24_HUMAN1-125
 
  2A:1-102
B:1-105

(-) Exons   (0, 0)

(no "Exon" information available for 4AZ9)

(-) 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:111
 aligned with SNX24_HUMAN | Q9Y343 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:111
                                     1                                                                                                     
                                     1        11        21        31        41        51        61        71        81        91       101 
          SNX24_HUMAN     - ---------MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV 102
               SCOP domains d4az9a_ A: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.......eeeeeeeeee..eeeeeeeehhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PX  PDB: A:1-102 UniProt: 1-125                                                                        PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4az9 A  -8 GTENLYFQSMEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNV 102
                                     1        11        21        31        41        51        61        71        81        91       101 

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with SNX24_HUMAN | Q9Y343 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:114
                                     1                                                                                                        
                                     1        11        21        31        41        51        61        71        81        91       101    
          SNX24_HUMAN     - ---------MEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHL 105
               SCOP domains d4az9b_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeeee.......eeeeeeeeee..eeeeeeehhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------PX  PDB: B:1-105 UniProt: 1-125                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4az9 B  -8 GTENLYFQSMEVYIPSFRYEESDLERGYTVFKIEVLMNGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHL 105
                                     1        11        21        31        41        51        61        71        81        91       101    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AZ9)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SNX24_HUMAN | Q9Y343)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0010314    phosphatidylinositol-5-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position.
biological process
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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