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(-) Description

Title :  FIRST AND SECOND IG DOMAINS FROM HUMAN ROBO1 (FORM 2)
 
Authors :  C. Morlot, S. Cusack, A. A. Mccarthy
Date :  25 Aug 07  (Deposition) - 25 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Proto-Oncogene, Differentiation, Phosphorylation, Disease Mutation, Neuronal Development, Immunoglobulin Domain, Chemotaxis, Neurogenesis, Glycoprotein, Transmembrane, Robo1, Membrane, Receptor, Ig Domain, Roundabout, Developmental Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Morlot, N. M. Thielens, R. B. Ravelli, W. Hemrika, R. A. Romijn, P. Gros, S. Cusack, A. A. Mccarthy
Structural Insights Into The Slit-Robo Complex.
Proc. Nat. Acad. Sci. Usa V. 104 14923 2007
PubMed-ID: 17848514  |  Reference-DOI: 10.1073/PNAS.0705310104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ROUNDABOUT HOMOLOG 1
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293-EBNA1
    Expression System Taxid9606
    Expression System VectorMODIFIED PTT3
    FragmentIG1-2M, RESIDUES 61-266
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymH-ROBO-1, DELETED IN U TWENTY TWENTY, ROBO1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:109 , ASP A:114 , ARG A:116 , ASP A:213 , GLU A:216 , ILE A:218 , THR A:219BINDING SITE FOR RESIDUE SO4 A1261
2AC2SOFTWAREASP A:76 , ASP A:160 , HOH A:2053BINDING SITE FOR RESIDUE SO4 A1262

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:89 -A:147
2A:191 -A:240

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:94 -Pro A:95
2His A:197 -Pro A:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V9R)

(-) Exons   (0, 0)

(no "Exon" information available for 2V9R)

(-) 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:197
 aligned with ROBO1_HUMAN | Q9Y6N7 from UniProtKB/Swiss-Prot  Length:1651

    Alignment length:197
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
          ROBO1_HUMAN    64 EDFPPRIVEHPSDLIVSKGEPATLNCKAEGRPTPTIEWYKGGERVETDKDDPRSHRMLLPSGSLFFLRIVHGRKSRPDEGVYVCVARNYLGEAVSHNASLEVAILRDDFRQNPSDVMVAVGEPAVMECQPPRGHPEPTISWKKDGSPLDDKDERITIRGGKLMITYTRKSDAGKYVCVGTNMVGERESEVAELTVLE 260
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------I-set-2v9rA01 A:170-258                                                                  -- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------I-set-2v9rA02 A:170-258                                                                  -- Pfam domains (2)
         Sec.struct. author ..eeeeeee....eee.....eee..eeeee...eeeeee..ee...........eee.....eee.............eeeeeeeee..eeee...eeeee.ee..........eeee....eeee.....ee...eeeeee..eee......eeee..eeee...hhhhheeeeeeeee..eeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9r A  64 EDFPPRIVEHPSDLIVSKGEPATLNCKAEGRPTPTIEWYKGGERVETDKDDPRSHRMLLPSGSLFFLRIVHGRKSRPDEGVYVCVARNYLGEAVSHDASLEVAILRDDFRQNPSDVMVAVGEPAVMECQPPRGHPEPTISWKKDGSPLDDKDERITIRGGKLMITYTRKSDAGKYVCVGTNMVGERESEVAELTVLE 260
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2V9R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V9R)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: I-set (67)
1aI-set-2v9rA01A:170-258
1bI-set-2v9rA02A:170-258

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ROBO1_HUMAN | Q9Y6N7)
molecular function
    GO:0030275    LRR domain binding    Interacting selectively and non-covalently with a LRR domain (leucine rich repeats) of a protein.
    GO:0008046    axon guidance receptor activity    Combining with an extracellular messenger and transmitting the signal from one side of the membrane to the other to results in a change in cellular activity involved in axon guidance.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0021836    chemorepulsion involved in postnatal olfactory bulb interneuron migration    The creation and reception of signals that repel olfactory bulb interneurons from the subventricular zone as a component process in tangential migration.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    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:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0070100    negative regulation of chemokine-mediated signaling pathway    Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of a chemokine binding to a cell surface receptor.
    GO:0033600    negative regulation of mammary gland epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of mammary gland epithelial cell proliferation.
    GO:0050925    negative regulation of negative chemotaxis    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism towards a lower concentration in a concentration gradient of a specific chemical.
    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:0035025    positive regulation of Rho protein signal transduction    Any process that activates or increases the frequency, rate or extent of Rho protein signal transduction.
    GO:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ROBO1_HUMAN | Q9Y6N72eo9 2v9q 2v9t 3wih 4hlj

(-) Related Entries Specified in the PDB File

2v9q FIRST AND SECOND IG DOMAINS FROM HUMAN ROBO1
2v9s SECOND LRR DOMAIN OF HUMAN SLIT2
2v9t COMPLEX BETWEEN THE SECOND LRR DOMAIN OF SLIT2 AND THE FIRST IG DOMAIN FROM ROBO1