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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE EPHRIN-B2 ECTODOMAIN
 
Authors :  J. Toth, T. Cutforth, A. D. Gelinas, K. A. Bethoney, J. Bard, C. J. Harris
Date :  03 May 01  (Deposition) - 03 May 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  P
Keywords :  Greek Key, Glycosylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Toth, T. Cutforth, A. D. Gelinas, K. A. Bethoney, J. Bard, C. J. Harrison
Crystal Structure Of An Ephrin Ectodomain.
Dev. Cell V. 1 83 2001
PubMed-ID: 11703926  |  Reference-DOI: 10.1016/S1534-5807(01)00002-8

(-) Compounds

Molecule 1 - EPHRIN-B2
    ChainsP
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPIC-ZALPHA
    Expression System Taxid4922
    Expression System VectorPLASMID
    FragmentECTODOMAIN, RESIDUES 30-207
    GeneEPHRIN-B2
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymEPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5, LERK-5, HTK LIGAND, HTK-L, ELF-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG P:2 , TYR P:37 , ASN P:39 , ASN P:42 , PRO P:66 , LYS P:67 , HOH P:222 , HOH P:255 , HOH P:285BINDING SITE FOR RESIDUE NAG P 1
2AC2SOFTWARENAG P:1 , MAN P:3 , TYR P:37 , LYS P:131 , HOH P:375BINDING SITE FOR RESIDUE NAG P 2
3AC3SOFTWARENAG P:2 , HOH P:367 , HOH P:375 , HOH P:379 , HOH P:386BINDING SITE FOR RESIDUE MAN P 3

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1P:65 -P:104
2P:92 -P:156

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPHRIN_RBD_2PS51551 Ephrin receptor-binding (ephrin RBD) domain profile.EFNB2_MOUSE31-167  1P:31-167
2EPHRIN_RBD_1PS01299 Ephrin receptor-binding (ephrin RBD) domain signature.EFNB2_MOUSE112-139  1P:112-139

(-) Exons   (0, 0)

(no "Exon" information available for 1IKO)

(-) 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 P from PDB  Type:PROTEIN  Length:141
 aligned with EFNB2_MOUSE | P52800 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:141
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169 
          EFNB2_MOUSE    30 SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCARPDQDVKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQD 170
               SCOP domains d1ikop_ P: Ephrin-b2 ectodomain                                                                                                               SCOP domains
               CATH domains 1ikoP00 P:30-170 Cupredoxins -  blue copper proteins                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.............eee......eeeee..............eeeeeehhhhhhhh.........eee.......eeeee................eeeeee.....hhhhh....hhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -EPHRIN_RBD_2  PDB: P:31-167 UniProt: 31-167                                                                                              --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------EPHRIN_RBD_1  PDB: P:112-139------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iko P  30 SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCARPDQDVKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQD 170
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169 

   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: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IKO)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (EFNB2_MOUSE | P52800)
molecular function
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    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:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    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:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0001945    lymph vessel development    The process whose specific outcome is the progression of a lymph vessel over time, from its formation to the mature structure.
    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:0010839    negative regulation of keratinocyte proliferation    Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population.
    GO:0072178    nephric duct morphogenesis    The process in which the anatomical structures of the nephric duct are generated and organized. A nephric duct is a tube that drains a primitive kidney.
    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:1903849    positive regulation of aorta morphogenesis    Any process that activates or increases the frequency, rate or extent of aorta morphogenesis.
    GO:2000727    positive regulation of cardiac muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation.
    GO:0050920    regulation of chemotaxis    Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
    GO:0048845    venous blood vessel morphogenesis    The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart.
cellular component
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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: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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        EFNB2_MOUSE | P528001kgy

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