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(-) Description

Title :  CRYSTAL STRUCTURE OF THE IMMUNORECEPTOR TIGIT IN COMPLEX WITH POLIOVIRUS RECEPTOR (PVR/CD155/NECL-5) D1 DOMAIN
 
Authors :  L. Rouge, K. F. Stengel, J. P. Yin, F. J. Bazan, C. Wiesmann
Date :  28 Oct 11  (Deposition) - 14 Mar 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pvr Tigit Igsf Signal Transduction Immunology, Igsf, Cell Surface Receptor Signalling, Glycosylation, Membrane Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. F. Stengel, K. Harden-Bowles, X. Yu, L. Rouge, J. Yin, L. Comps-Agrar, C. Wiesmann, J. F. Bazan, D. L. Eaton, J. L. Grogan
Structure Of Tigit Immunoreceptor Bound To Poliovirus Receptor Reveals A Cell-Cell Adhesion And Signaling Mechanism That Requires Cis-Trans Receptor Clustering.
Proc. Natl. Acad. Sci. Usa V. 109 5399 2012
PubMed-ID: 22421438  |  Reference-DOI: 10.1073/PNAS.1120606109

(-) Compounds

Molecule 1 - T CELL IMMUNORECEPTOR WITH IG AND ITIM DOMAINS
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentTIGIT, UNP RESIDUES 20-128
    GeneTIGIT, VSIG9, VSTM3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymV-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 9, V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 3
 
Molecule 2 - POLIOVIRUS RECEPTOR
    ChainsC, D
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    FragmentPVR, UNP RESIDUES 28-145
    GenePVR, PVS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNECTIN-LIKE PROTEIN 5, NECL-5

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR D:50 , ASN D:105BINDING SITE FOR RESIDUE NAG D 19
2AC2SOFTWAREGLY C:119 , ASN C:120 , TRP C:138BINDING SITE FOR RESIDUE NAG C 19
3AC3SOFTWAREASN D:120 , TRP D:138BINDING SITE FOR RESIDUE NAG D 146
4AC4SOFTWAREASN C:105 , SER C:107BINDING SITE FOR RESIDUE NAG C 146

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:108
2B:45 -B:108
3C:49 -C:123
4D:49 -D:123

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:88 -Pro A:89
2Tyr A:113 -Pro A:114
3Gly B:88 -Pro B:89
4Tyr B:113 -Pro B:114
5Phe C:128 -Pro C:129
6Phe D:128 -Pro D:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_056079I33VTIGIT_HUMANPolymorphism13098836A/BI33V
2UniProtVAR_003952A67TPVR_HUMANPolymorphism1058402C/DA67T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UDW)

(-) Exons   (0, 0)

(no "Exon" information available for 3UDW)

(-) 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:105
 aligned with TIGIT_HUMAN | Q495A1 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:105
                                    32        42        52        62        72        82        92       102       112       122     
          TIGIT_HUMAN    23 MTGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAICNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEVL 127
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee.......eee.eeee....eeeeeeee....eeeeee...eeee...hhh.eee.....eee...hhhhheeeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------V---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3udw A  23 MTGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAICNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEVL 127
                                    32        42        52        62        72        82        92       102       112       122     

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with TIGIT_HUMAN | Q495A1 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:103
                                    33        43        53        63        73        83        93       103       113       123   
          TIGIT_HUMAN    24 TGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAICNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEV 126
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee......eee.eeee....eeeeeeeee..eeeeeee...eeee...hhh.eee.....eee...hhhhheeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------V--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3udw B  24 TGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAICNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEV 126
                                    33        43        53        63        73        83        93       103       113       123   

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with PVR_HUMAN | P15151 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:116
                                    37        47        57        67        77        87        97       107       117       127       137      
            PVR_HUMAN    28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLA 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeee....eee..eee.......eeeeeeeee.......eeee...eeee.....eee.............eee...hhhhheeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------T---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3udw C  28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVLA 143
                                    37        47        57        67        77        87        97       107       117       127       137      

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with PVR_HUMAN | P15151 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:115
                                    37        47        57        67        77        87        97       107       117       127       137     
            PVR_HUMAN    28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVL 142
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eee..eee.......eeeeeeeee.......eeee...eeee.....eee.............eee...hhhhheeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------T--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3udw D  28 DVVVQAPTQVPGFLGDSVTLPCYLQVPNMEVTHVSQLTWARHGESGSMAVFHQTQGPSYSESKRLEFVAARLGAELRNASLRMFGLRVEDEGNYTCLFVTFPQGSRSVDIWLRVL 142
                                    37        47        57        67        77        87        97       107       117       127       137     

   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  (0, 0)

(no "SCOP Domain" information available for 3UDW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UDW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UDW)

(-) Gene Ontology  (32, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TIGIT_HUMAN | Q495A1)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    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:0050868    negative regulation of T cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation.
    GO:0032695    negative regulation of interleukin-12 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
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: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.

Chain C,D   (PVR_HUMAN | P15151)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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: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: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:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    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: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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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)

UniProtKB/Swiss-Prot
        PVR_HUMAN | P151511dgi 1nn8 3epc 3epd 3epf 3j8f 3j9f 3uro 4fqp
        TIGIT_HUMAN | Q495A13q0h 3rq3 3ucr 5v52

(-) Related Entries Specified in the PDB File

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