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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PX DOMAIN OF HUMAN SORTING NEXIN 3
 
Authors :  P. Canning, W. Kiyani, D. S. Froese, T. Krojer, C. Strain-Damerell, F. V C. H. Arrowsmith, A. M. Edwards, C. Bountra, W. W. Yue
Date :  31 Oct 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein Transport, Endosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Canning, D. S. Froese, T. Krojer, C. Strain-Damerell, F. Von Delft C. H. Arrowsmith, A. M. Edwards, C. Bountra, W. W. Yue
Crystal Structure Of The Px Domain Of Human Sorting Nexin 3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SORTING NEXIN-3
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentPX DOMAIN, RESIDUES 24-155
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMGC
    SynonymPROTEIN SDP3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YPS)

(-) Sites  (0, 0)

(no "Site" information available for 2YPS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YPS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YPS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YPS)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX3_HUMAN27-151
 
 
 
  4A:27-148
B:27-148
C:27-147
D:27-150
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX3_HUMAN27-151
 
 
 
  1A:27-148
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX3_HUMAN27-151
 
 
 
  1-
B:27-148
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX3_HUMAN27-151
 
 
 
  1-
-
C:27-147
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX3_HUMAN27-151
 
 
 
  1-
-
-
D:27-150

(-) Exons   (0, 0)

(no "Exon" information available for 2YPS)

(-) 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:107
 aligned with SNX3_HUMAN | O60493 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:127
                                    31        41        51        61        71        81        91       101       111       121       131       141       
           SNX3_HUMAN    22 YGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDE 148
               SCOP domains d2ypsa_ A: auto     mated matches                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..-----.hhhhh.eeeeeee........eeeeeehhhhhhhhhhhhhhhh............---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PX  PDB: A:27-148 UniProt: 27-151                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yps A  -1 SMPPSNFLEIDVSNP-----GRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAF---------------NFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDE 148
                             ||     31    |    -|       51        61        71        81        91     |   -         - |     121       131       141       
                             0|          36    42                                                     97             113                                   
                             24                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:102
 aligned with SNX3_HUMAN | O60493 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:122
                                    36        46        56        66        76        86        96       106       116       126       136       146  
           SNX3_HUMAN    27 NFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDE 148
               SCOP domains d2ypsb_ B      : automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.------.hhhh.eeeeeeee........eeeeeeehhhhhhhhhhhhhhh............--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PX  PDB: B:27-148 UniProt: 27-151                                                                                          PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yps B  27 NFLEIDVSN------GRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAF--------------DNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDE 148
                                    |-     |  46        56        66        76        86        96|        -     | 116       126       136       146  
                                   35     42                                                     97            112                                    

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with SNX3_HUMAN | O60493 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:121
                                    36        46        56        66        76        86        96       106       116       126       136       146 
           SNX3_HUMAN    27 NFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQD 147
               SCOP domains d2ypsc_ C      : automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.------.hhhh.eeeeeeee........eeeeeeehhhhhhhhhhhhhhh...........-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PX  PDB: C:27-147 UniProt: 27-151                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yps C  27 NFLEIDVSN------GRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKA-----------------FIEERKQGLEQFINKVAGHPLAQNERCLHMFLQD 147
                                    |-     |  46        56        66        76        86        96         -       116       126       136       146 
                                   35     42                                                    96               114                                 

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with SNX3_HUMAN | O60493 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:124
                                    36        46        56        66        76        86        96       106       116       126       136       146    
           SNX3_HUMAN    27 NFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEII 150
               SCOP domains d2ypsd_ D      : automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.------.hhhh.eeeeeeee........eeeeeeehhhhhhhhhhhhhhh...........-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PX  PDB: D:27-150 UniProt: 27-151                                                                                            PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yps D  27 NFLEIDVSN------GRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKA-----------------FIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEII 150
                                    |-     |  46        56        66        76        86        96         -       116       126       136       146    
                                   35     42                                                    96               114                                    

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YPS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YPS)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SNX3_HUMAN | O60493)
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:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0070676    intralumenal vesicle formation    The invagination of the endosome membrane and resulting formation of a vesicle within the lumen of the endosome.
    GO:0010324    membrane invagination    The infolding of a membrane.
    GO:2000642    negative regulation of early endosome to late endosome transport    Any process that stops, prevents or reduces the frequency, rate or extent of early endosome to late endosome transport.
    GO:0050765    negative regulation of phagocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
    GO:0042177    negative regulation of protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0051224    negative regulation of protein transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0046597    negative regulation of viral entry into host cell    Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0022615    protein to membrane docking    The initial attachment of a protein to a target membrane, mediated by a proteins protruding from the target membrane. Docking requires only that the proteins come close enough to interact and adhere.
    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:0030111    regulation of Wnt signaling pathway    Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    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:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0032009    early phagosome    A membrane-bounded intracellular vesicle as initially formed upon the ingestion of particulate material by phagocytosis.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0030904    retromer complex    A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.

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 Related Entries

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

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        SNX3_HUMAN | O604932mxc 5f0j 5f0l 5f0m 5f0p

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