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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SNX17 PX DOMAIN WITH BOUND SULPHATE
 
Authors :  R. Ghai, B. M. Collins
Date :  17 Feb 10  (Deposition) - 02 Mar 10  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Snx17, Sorting Nexin, Px Domain, Endosome, Phosphoprotein, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Ghai, M. Mobli, S. J. Norwood, A. Bugarcic, R. D. Teasdale, G. F. King B. M. Collins
Phox Homology Band 4. 1/Ezrin/Radixin/Moesin-Like Proteins Function As Molecular Scaffolds That Interact With Cargo Receptors And Ras Gtpases
Proc. Natl. Acad. Sci. Usa 2011
PubMed-ID: 21512128  |  Reference-DOI: 10.1073/PNAS.1017110108

(-) Compounds

Molecule 1 - SORTING NEXIN-17
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET BASED LIGATION-INDEPENDENT VECTOR
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSNX17 PX DOMAIN (RESIDUES 1-112)
    GeneSNX17
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSNX17

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , TYR A:37 , SER A:38 , HOH A:118 , HOH A:129 , HOH A:131 , HOH A:218 , HOH A:389BINDING SITE FOR RESIDUE SO4 A 113
2AC2SOFTWARELYS A:49 , ARG B:48BINDING SITE FOR RESIDUE SO4 A 114
3AC3SOFTWAREARG B:36 , TYR B:37 , SER B:38 , HOH B:119 , HOH B:125 , HOH B:146 , HOH B:405 , HOH B:437BINDING SITE FOR RESIDUE SO4 B 113
4AC4SOFTWAREGLN A:74 , ARG B:48 , ALA B:53 , HOH B:369 , HOH B:392BINDING SITE FOR RESIDUE SO4 B 114
5AC5SOFTWARELYS B:63 , GLN B:78 , HOH B:364 , HOH B:436 , HOH B:465 , HOH B:503BINDING SITE FOR RESIDUE SO4 B 115
6AC6SOFTWAREARG C:36 , TYR C:37 , SER C:38 , HOH C:116 , HOH C:131 , HOH C:483 , HOH C:487BINDING SITE FOR RESIDUE SO4 C 113

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LUI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser C:15 -Gly C:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX17_HUMAN1-109
 
  2B:1-109
C:1-109
Biological Unit 1 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX17_HUMAN1-109
 
  0-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX17_HUMAN1-109
 
  1B:1-109
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX17_HUMAN1-109
 
  1-
C:1-109

(-) Exons   (0, 0)

(no "Exon" information available for 3LUI)

(-) 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:104
 aligned with SNX17_HUMAN | Q15036 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:109
                                    11        21        31        41        51        61        71        81        91       101         
          SNX17_HUMAN     2 HFSIPETESRSGDSGGSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQETQ 110
               SCOP domains d3luia_ A:      automated matches                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.-----..eeeeeeee..eeeeeeehhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PX  PDB: - UniProt: 1-109                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3lui A   2 HFSIPETESRS-----SAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQETQ 110
                                    11|     | 21        31        41        51        61        71        81        91       101         
                                     12    18                                                                                            

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with SNX17_HUMAN | Q15036 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
          SNX17_HUMAN     1 MHFSIPETESRSGDSGGSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQETQQ 111
               SCOP domains d3luib_ B:      automated matches                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee-----...eeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PX  PDB: B:1-109 UniProt: 1-109                                                                              -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3lui B   1 MHFSIPETESR-----GSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQETQQ 111
                                    10|     | 20        30        40        50        60        70        80        90       100       110 
                                     11    17                                                                                              

Chain C from PDB  Type:PROTEIN  Length:109
 aligned with SNX17_HUMAN | Q15036 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:111
                              1                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108 
          SNX17_HUMAN     - --MHFSIPETESRSGDSGGSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQET 109
               SCOP domains d3luic_ C: aut  omated matches                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---PX-3luiC01   C:2-105                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ---PX-3luiC02   C:2-105                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ---PX-3luiC03   C:2-105                                                                                    ---- Pfam domains (3)
         Sec.struct. author ....eeeeeeeee.--.....eeeeeeee..eeeeeehhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --PX  PDB: C:1-109 UniProt: 1-109                                                                               PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3lui C  -1 NAMHFSIPETESRS--SGGSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQET 109
                                     8   |  | 18        28        38        48        58        68        78        88        98       108 
                                        12 15                                                                                              

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Family: PX (17)
1aPX-3luiC01C:2-105
1bPX-3luiC02C:2-105
1cPX-3luiC03C:2-105

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SNX17_HUMAN | Q15036)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0035904    aorta development    The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0003279    cardiac septum development    The progression of a cardiac septum over time, from its initial formation to the mature structure.
    GO:0006707    cholesterol catabolic process    The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    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:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:1990126    retrograde transport, endosome to plasma membrane    The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    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:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SNX17_HUMAN | Q150363fog 4gxb 4tkn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LUI)