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(-) Description

Title :  SO4 BOUND PX-BAR MEMBRANE REMODELING UNIT OF SORTING NEXIN 9
 
Authors :  O. Pylypenko, R. Lundmark, E. Rasmuson, S. R. Carlsson, A. Rak
Date :  16 Sep 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sorting Nexin, Membrane Transport, Px Domain, Bar Domain, Tubulation, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pylypenko, R. Lundmark, E. Rasmuson, S. R. Carlsson, A. Rak
The Px-Bar Membrane-Remodeling Unit Of Sorting Nexin 9
Embo J. V. 26 4788 2007
PubMed-ID: 17948057  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601889
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SORTING NEXIN-9
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-2
    Expression System StrainBL21 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FRAGMENT, RESIDUES 214-594
    GeneSNX9, SH3PX1, SH3PXD3A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSH3 AND PX DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:286 , TYR A:287 , LYS A:288BINDING SITE FOR RESIDUE SO4 A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX9_HUMAN250-361  1A:250-361
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.SNX9_HUMAN250-361  2A:250-361

(-) Exons   (12, 12)

Asymmetric Unit (12, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003921851ENSE00001381139chr6:158244296-158244478183SNX9_HUMAN1-440--
1.2ENST000003921852ENSE00001434680chr6:158288579-15828866587SNX9_HUMAN5-33290--
1.3ENST000003921853ENSE00000894254chr6:158294134-15829420875SNX9_HUMAN34-58250--
1.4ENST000003921854ENSE00000894253chr6:158296083-158296208126SNX9_HUMAN59-100420--
1.5ENST000003921855ENSE00000894252chr6:158317859-158318030172SNX9_HUMAN101-158580--
1.6ENST000003921856ENSE00000894251chr6:158322930-158323077148SNX9_HUMAN158-207500--
1.7ENST000003921857ENSE00000894250chr6:158327160-15832724485SNX9_HUMAN207-235291A:214-23522
1.8ENST000003921858ENSE00000894249chr6:158330697-158330822126SNX9_HUMAN236-277421A:236-27742
1.9ENST000003921859ENSE00000894248chr6:158330940-158331057118SNX9_HUMAN278-317401A:278-31740
1.10ENST0000039218510ENSE00000894247chr6:158342563-158342693131SNX9_HUMAN317-360441A:317-36044
1.11ENST0000039218511ENSE00000894246chr6:158348143-158348246104SNX9_HUMAN361-395351A:361-39535
1.12ENST0000039218512ENSE00000894245chr6:158349631-158349734104SNX9_HUMAN395-430361A:395-43036
1.13ENST0000039218513ENSE00000894244chr6:158353227-15835330478SNX9_HUMAN430-456271A:430-45627
1.14ENST0000039218514ENSE00000894243chr6:158356996-15835707277SNX9_HUMAN456-481261A:456-48126
1.15ENST0000039218515ENSE00001218186chr6:158358466-15835855590SNX9_HUMAN482-511301A:482-51130
1.16ENST0000039218516ENSE00001218176chr6:158359665-158359779115SNX9_HUMAN512-550391A:512-55039
1.17ENST0000039218517ENSE00000830242chr6:158361915-15836200692SNX9_HUMAN550-580311A:550-58031
1.18ENST0000039218518ENSE00001139578chr6:158363823-1583661092287SNX9_HUMAN581-595151A:581-59515

(-) 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:382
 aligned with SNX9_HUMAN | Q9Y5X1 from UniProtKB/Swiss-Prot  Length:595

    Alignment length:382
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593  
           SNX9_HUMAN   214 PGTEQYLLAKQLAKPKEKIPIIVGDYGPMWVYPTSTFDCVVADPRKGSKMYGLKSYIEYQLTPTNTNRSVNHRYKHFDWLYERLLVKFGSAIPIPSLPDKQVTGRFEEEFIKMRMERLQAWMTRMCRHPVISESEVFQQFLNFRDEKEWKTGKRKAERDELAGVMIFSTMEPEAPDLDLVEIEQKCEAVGKFTKAMDDGVKELLTVGQEHWKRCTGPLPKEYQKIGKALQSLATVFSSSGYQGETDLNDAITEAGKTYEEIASLVAEQPKKDLHFLMECNHEYKGFLGCFPDIIGTHKGAIEKVKESDKLVATSKITLQDKQNMVKRVSIMSYALQAEMNHFHSNRIYDYNSVIRLYLEQQVQFYETIAEKLRQALSRFPVM 595
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------PX-2rajA02 A:247-357                                                                                           BAR_3_WASP_bdg-2rajA01 A:358-593                                                                                                                                                                                                            -- Pfam domains
         Sec.struct. author hhhhhhhhh.........eeeeee..eeee........eeeeeeeee........eeeeeeee......eeeehhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PX  PDB: A:250-361 UniProt: 250-361                                                                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7 [INCOMPLETE] Exon 1.8  PDB: A:236-277 UniProt: 236-277 ---------------------------------------Exon 1.10  PDB: A:317-360 UniProt: 317-360  Exon 1.11  PDB: A:361-395          ----------------------------------Exon 1.13  PDB: A:430-456  -------------------------Exon 1.15  PDB: A:482-511     Exon 1.16  PDB: A:512-550              ------------------------------Exon 1.18       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9  PDB: A:278-317                -----------------------------------------------------------------------------Exon 1.12  PDB: A:395-430           -------------------------Exon 1.14  PDB: A:456-481 --------------------------------------------------------------------Exon 1.17  PDB: A:550-580      --------------- Transcript 1 (2)
                 2raj A 214 PGTEQYLLAKQLAKPKEKIPIIVGDYGPMWVYPTSTFDCVVADPRKGSKMYGLKSYIEYQLTPTNTNRSVNHRYKHFDWLYERLLVKFGSAIPIPSLPDKQVTGRFEEEFIKMRMERLQAWMTRMCRHPVISESEVFQQFLNFRDEKEWKTGKRKAERDELAGVMIFSTMEPEAPDLDLVEIEQKCEAVGKFTKAMDDGVKELLTVGQEHWKRCTGPLPKEYQKIGKALQSLATVFSSSGYQGETDLNDAITEAGKTYEEIASLVAEQPKKDLHFLMECNHEYKGFLGCFPDIIGTHKGAIEKVKESDKLVATSKITLQDKQNMVKRVSIMSYALQAEMNHFHSNRIYDYNSVIRLYLEQQVQFYETIAEKLRQALSRFPVM 595
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593  

   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 2RAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Family: PX (17)

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)
Chain A   (SNX9_HUMAN | Q9Y5X1)
molecular function
    GO:0005545    1-phosphatidylinositol binding    Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0071933    Arp2/3 complex binding    Interacting selectively and non-covalently with an Arp2/3 complex, a protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5).
    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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0036089    cleavage furrow formation    Generation of the cleavage furrow, a shallow groove in the cell surface near the old metaphase plate that marks the site of cytokinesis. This process includes the recruitment and localized activation of signals such as RhoA at the site of the future furrow to ensure that furrowing initiates at the correct site in the cell.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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:0060988    lipid tube assembly    The aggregation, arrangement and bonding together of a set of macromolecules to form a macromolecular complex that contains a tube of lipid surrounded by a protein coat involved in membrane shaping of vesicle membranes as they fuse or undergo fission.
    GO:0000281    mitotic cytokinesis    A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
    GO:0097320    plasma membrane tubulation    A membrane tubulation process occurring in a plasma membrane.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0051044    positive regulation of membrane protein ectodomain proteolysis    Any process that activates or increases the frequency, rate or extent of membrane protein ectodomain peptidolysis.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    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: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.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SNX9_HUMAN | Q9Y5X12rai 2rak 3dyt 3dyu 3lge

(-) Related Entries Specified in the PDB File

2rai 2rak