Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THIRD LRR DOMAIN OF DROSOPHILA SLIT
 
Authors :  J. A. Howitt, N. J. Clout, E. Hohenester
Date :  17 Sep 04  (Deposition) - 25 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein, Secreted Protein, Axon Guidance, Leucine-Rich Repeat Glycoprotein, Egf-Like Domain, Signal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Howitt, N. J. Clout, E. Hohenester
Binding Site For Robo Receptors Revealed By Dissection Of The Leucine-Rich Repeat Region Of Slit.
Embo J. V. 23 4406 2004
PubMed-ID: 15496984  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600446

(-) Compounds

Molecule 1 - SLIT PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemHUMAN
    Expression System Cell Line293-EBNA
    Expression System PlasmidPCEP-PU
    Expression System Taxid9606
    FragmentTHIRD LRR DOMAIN, RESIDUES 542-733
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1W8A)

(-) Sites  (0, 0)

(no "Site" information available for 1W8A)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:543 -A:549
2A:547 -A:556
3A:657 -A:733
4A:681 -A:704
5A:683 -A:725

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W8A)

(-) PROSITE Motifs  (1, 5)

Asymmetric/Biological Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.SLIT_DROME101-122
125-146
149-170
173-194
197-218
221-242
245-266
347-368
371-392
395-416
419-440
443-464
571-592
596-617
620-641
644-665
668-689
791-812
839-860
815-836
  5-
-
-
-
-
-
-
-
-
-
-
-
A:571-592
A:596-617
A:620-641
A:644-665
A:668-689
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1W8A)

(-) Sequences/Alignments

Asymmetric/Biological 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:189
 aligned with SLIT_DROME | P24014 from UniProtKB/Swiss-Prot  Length:1504

    Alignment length:192
                                   551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731  
           SLIT_DROME   542 DCPAMCHCEGTTVDCTGRGLKEIPRDIPLHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNCNCHLAWFAEWLRKKSLNGGAARCGAPSKVRDVQIKDLPHSEFKCSSENSEGC 733
               SCOP domains d1w8aa_ A: Slit                                                                                                                                                                                  SCOP domains
               CATH domains 1w8aA00 A:542-733 Ribonuclease Inhibitor                                                                                                                                                         CATH domains
               Pfam domains LRRNT-1w8aA03 A:542-569     -------------------------------------------------LRR_8-1w8aA01 A:619-679                                      ---------------------LRRCT-1w8aA02 A:701-726   ------- Pfam domains
         Sec.struct. author ......eee..eee..................eee.............hhhhh....eee.....................eee.......ee............eee.......ee............eee........hhhhhhhhhhhhhhh.hhhhh............hhhh.........---... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------LRR  PDB: A:571-592   ---LRR  PDB: A:596-617   --LRR  PDB: A:620-641   --LRR  PDB: A:644-665   --LRR  PDB: A:668-689   -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w8a A 542 DCPAMCHCEGTTVDCTGRGLKEIPRDIPLHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNCNCHLAWFAEWLRKKSLNGGAARCGAPSKVRDVQIKDLPHSEFKCSS---EGC 733
                                   551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721     | 731  
                                                                                                                                                                                                                   727 731  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: LRR (77)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLIT_DROME | P24014)
molecular function
    GO:0048495    Roundabout binding    Interacting selectively and non-covalently with the Roundabout (ROBO) receptor, a transmembrane receptor.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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).
biological process
    GO:0035385    Roundabout signaling pathway    A series of molecular signals initiated by the binding of a SLIT protein to a Roundabout (ROBO) family receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0048846    axon extension involved in axon guidance    The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0016199    axon midline choice point recognition    The recognition of molecules at the central nervous system midline choice point by an axon growth cone; this choice point determines whether the growth cone will cross the midline.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0007502    digestive tract mesoderm development    The process whose specific outcome is the progression of the digestive tract mesoderm over time, from its formation to the mature structure. The digestive tract mesoderm is portion of the middle layer of the three primary germ layers of the embryo which will go on to form part of the digestive tract of the organism.
    GO:0035050    embryonic heart tube development    The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
    GO:0007427    epithelial cell migration, open tracheal system    The orderly movement of epithelial cells during development of an open tracheal system. An example of this is found in Drosophila melanogaster.
    GO:0008347    glial cell migration    The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
    GO:0008406    gonad development    The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
    GO:0050929    induction of negative chemotaxis    Any process that initiates the directed movement of a motile cell or organism towards a lower concentration in a concentration gradient of a specific chemical.
    GO:0046331    lateral inhibition    Signaling between cells of equivalent developmental potential that results in these cells adopting different developmental fates. An example is the suppression by cells with a particular fate of the adoption of the same fate by surrounding cells.
    GO:0007509    mesoderm migration involved in gastrulation    The migration of mesodermal cells during gastrulation to help establish the multilayered body plan of the organism.
    GO:0008078    mesodermal cell migration    The orderly movement of mesodermal cells from one site to another.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0001764    neuron migration    The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
    GO:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0022409    positive regulation of cell-cell adhesion    Any process that activates or increases the rate or extent of cell adhesion to another cell.
    GO:0050770    regulation of axonogenesis    Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
    GO:0010632    regulation of epithelial cell migration    Any process that modulates the frequency, rate or extent of epithelial cell migration.
    GO:2000274    regulation of epithelial cell migration, open tracheal system    Any process that modulates the frequency, rate or extent of epithelial cell migration, open tracheal system.
    GO:0007432    salivary gland boundary specification    Determination of where the salivary gland forms, the total number of salivary gland cells and how many cells are allocated to each of the specialised cell types within the salivary gland.
cellular component
    GO:0071666    Slit-Robo signaling complex    A protein-carbohydrate complex that consists of a transmembrane roundabout (Robo) receptor, an extracellular Slit ligand and heparin/heparan sulfate.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1w8a)
 
  Sites
(no "Sites" information available for 1w8a)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1w8a)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1w8a
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SLIT_DROME | P24014
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SLIT_DROME | P24014
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1W8A)

(-) Related Entries Specified in the PDB File

1ozn NOGO RECEPTOR LIGAND BINDING DOMAIN