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(-) Description

Title :  NMR SOLUTION STRUCTURE OF HUMAN EPHRINB2 ECTODOMAIN
 
Authors :  X. Ran, J. Fan, J. Song
Date :  01 Sep 06  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Ephrinb2 Ectodomain, Nmr Solution Structure, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Ran, J. Fan, J. Song
Nmr Solution Structure Of Human Ephrinb2 Ectodomain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPHRIN-B2
    Cell LineHELA CELLS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-32A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentECTODOMAIN, RESIDUES 1-142
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEPH-RELATED RECEPTOR TYROSINE KINASE LIGAND 5, LERK-5, HTK LIGAND, HTK-L

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2I85)

(-) Sites  (0, 0)

(no "Site" information available for 2I85)

(-) SS Bonds  (2, 2)

NMR Structure
No.Residues
1A:38 -A:77
2A:65 -A:129

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I85)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I85)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EPHRIN_RBD_2PS51551 Ephrin receptor-binding (ephrin RBD) domain profile.EFNB2_HUMAN28-164  1A:4-140
2EPHRIN_RBD_1PS01299 Ephrin receptor-binding (ephrin RBD) domain signature.EFNB2_HUMAN109-136  1A:85-112

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002453231aENSE00001931658chr13:107187462-107187191272EFNB2_HUMAN1-41411A:1-1717
1.2ENST000002453232ENSE00001654984chr13:107165160-107164877284EFNB2_HUMAN41-136961A:17-11296
1.3ENST000002453233ENSE00000995278chr13:107148188-10714809693EFNB2_HUMAN136-167321A:112-14231
1.4ENST000002453234ENSE00000854052chr13:107147342-107147229114EFNB2_HUMAN167-205390--
1.5bENST000002453235bENSE00001923391chr13:107145776-1071420933684EFNB2_HUMAN205-3331290--

(-) Sequences/Alignments

NMR Structure
   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:142
 aligned with EFNB2_HUMAN | P52799 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:142
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164  
          EFNB2_HUMAN    25 SKSIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQ 166
               SCOP domains d2i85a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee............eeee......eeeeee.............eeeee.hhhhhhhh.........eee......eeeeee................eeeeee.....hhhhh.............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---EPHRIN_RBD_2  PDB: A:4-140 UniProt: 28-164                                                                                               -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------EPHRIN_RBD_1  PDB: A:85-112 ------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1a        ----------------------------------------------------------------------------------------------Exon 1.3  PDB: A:112-142        Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.2  PDB: A:17-112 UniProt: 41-136                                                         ------------------------------ Transcript 1 (2)
                 2i85 A   1 SKSIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQ 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  

   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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I85)

(-) Gene Ontology  (29, 29)

NMR Structure(hide GO term definitions)
Chain A   (EFNB2_HUMAN | P52799)
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.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
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:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    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: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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    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: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:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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: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)

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        EFNB2_HUMAN | P527992hle 2vsk 2vsm 2wo2 3gxu 4uf7

(-) Related Entries Specified in the PDB File

1iko CRYSTAL STRUCTURE OF THE SAME PROTEIN FROM MOUSE