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(-) Description

Title :  CRYSTAL STRUCTURE OF CELL ADHESION MOLECULE NECTIN-2/CD112 MUTANT FAMP
 
Authors :  J. Liu, X. Qian, Z. Chen, X. Xu, F. Gao, S. Zhang, R. Zhang, J. Qi, G. F. Gao,
Date :  23 Jan 12  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Adhesion, Cd226, Cell Surface (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Liu, X. Qian, Z. Chen, X. Xu, F. Gao, S. Zhang, R. Zhang, J. Qi, G. F. Gao J. Yan
Crystal Structure Of Cell Adhesion Molecule Nectin-2/Cd112 And Its Binding To Immune Receptor Dnam-1/Cd226
J. Immunol. V. 188 5511 2012
PubMed-ID: 22547693  |  Reference-DOI: 10.4049/JIMMUNOL.1200324

(-) Compounds

Molecule 1 - POLIOVIRUS RECEPTOR-RELATED PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentIG-LIKE V-TYPE DOMAIN, UNP RESIDUES 32-158
    GenePVRL2, HVEB, PRR2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHERPES VIRUS ENTRY MEDIATOR B, HERPESVIRUS ENTRY MEDIATOR B, HVEB, NECTIN-2

 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 4DFI)

(-) Sites  (0, 0)

(no "Site" information available for 4DFI)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:24 -A:110

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:27 -Pro A:28
2Lys A:67 -Pro A:68
3Ser A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DFI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DFI)

(-) Exons   (0, 0)

(no "Exon" information available for 4DFI)

(-) 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:124
 aligned with NECT2_HUMAN | Q92692 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:128
                                    40        50        60        70        80        90       100       110       120       130       140       150        
          NECT2_HUMAN    31 AQDVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKMGPSFPSPKPGSERLSFVSAKQSTGQDTEAELQDATLALHGLTVEDEGNYTCEFATFPKGSVRGMTWLRV 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eee......eee..eee......eeeeeeee....hhhh.eeeeee...eee......hhh.eee.......----........eee...hhhhheeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfi A   1 MQDVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKSGPSFSSPKPGSERLSFVSAKQST----EAELQDATLALHGLTVEDEGNYTCEFSTSPKGSVRGMTWLRV 128
                                    10        20        30        40        50        60        70        80 |    | 90       100       110       120        
                                                                                                            82   87                                         

   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 4DFI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DFI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DFI)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NECT2_HUMAN | Q92692)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0015026    coreceptor activity    Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0001675    acrosome assembly    The formation of the acrosome from the spermatid Golgi.
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    GO:0044406    adhesion of symbiont to host    The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0032990    cell part morphogenesis    The process in which the anatomical structures of a cell part are generated and organized.
    GO:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    GO:0044782    cilium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
    GO:0046814    coreceptor-mediated virion attachment to host cell    The process by which a virion attaches to a host cell by binding to a co-receptor on the host cell surface.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0051654    establishment of mitochondrion localization    The directed movement of the mitochondrion to a specific location.
    GO:0009566    fertilization    The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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:0002891    positive regulation of immunoglobulin mediated immune response    Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response.
    GO:0033005    positive regulation of mast cell activation    Any process that activates or increases the frequency, rate, or extent of mast cell activation.
    GO:0045954    positive regulation of natural killer cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
    GO:0002860    positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target    Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated cytotoxicity directed against tumor cell target.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0046596    regulation of viral entry into host cell    Any process that modulates the frequency, rate or extent of the viral entry into the host cell.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0030382    sperm mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of sperm mitochondria; the process in which they take on their characteristic morphology; they are flattened, elongated, and arranged circumferentially into a tight helical coil around the tail-dense fibers of the mature sperm.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    GO:0007289    spermatid nucleus differentiation    The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization.
    GO:0060370    susceptibility to T cell mediated cytotoxicity    The process of causing a cell to become susceptible to T cell mediated cytotoxicity.
    GO:0042271    susceptibility to natural killer cell mediated cytotoxicity    The process of causing a cell to become susceptible to natural killer cell mediated cytotoxicity.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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: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.
    GO:0005915    zonula adherens    A cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.

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

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        NECT2_HUMAN | Q926923r0n 4dfh 4hza 5v52

(-) Related Entries Specified in the PDB File

4dfh