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(-) Description

Title :  CRYSTAL STRUCTURE OF LIR-2 (ILT4) AT 1.8 : DIFFERENCES FROM LIR-1 (ILT2) IN REGIONS IMPLICATED IN THE BINDING OF THE CYTOMEGALOVIRUS CLASS I MHC HOMOLOG UL18
 
Authors :  B. E. Willcox, L. M. Thomas, T. L. Chapman, A. P. Heikema, A. P. West, P. J.
Date :  03 May 06  (Deposition) - 20 Jun 06  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Ig Like Domains, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. E. Willcox, L. M. Thomas, T. L. Chapman, A. P. Heikema, A. P. West, P. J. Bjorkman
Crystal Structure Of Lir-2 (Ilt4) At 1. 8 A: Differences Fro Lir-1 (Ilt2) In Regions Implicated In The Binding Of The Human Cytomegalovirus Class I Mhc Homolog Ul18.
Bmc Struct. Biol. V. 2 6 2002
PubMed-ID: 12390682  |  Reference-DOI: 10.1186/1472-6807-2-6

(-) Compounds

Molecule 1 - LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR SUBFAMILY B MEMBER 2 PRECURSOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAINS 1 AND 2
    GeneLILRB2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 2, LIR-2, IMMUNOGLOBULIN- LIKE TRANSCRIPT 4, ILT-4, MONOCYTE/MACROPHAGE IMMUNOGLOBULIN-LIKE RECEPTOR 10, MIR-10, CD85D ANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:40 , ARG A:72 , TYR A:73 , GLY A:74 , LEU A:87BINDING SITE FOR RESIDUE IPA A 501

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:75
2A:122 -A:174
3A:134 -A:144

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:11 -Pro A:12
2Gln A:107 -Pro A:108
3Gly A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GW5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GW5)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003917491aENSE00001932163chr19:54785039-54784816224LIRB2_HUMAN-00--
1.3aENST000003917493aENSE00002181459chr19:54784399-5478431882LIRB2_HUMAN1-12120--
1.4bENST000003917494bENSE00001756910chr19:54784154-5478411936LIRB2_HUMAN12-24130--
1.5bENST000003917495bENSE00000897438chr19:54783930-54783646285LIRB2_HUMAN24-119961A:3-97 (gaps)95
1.6ENST000003917496ENSE00001707191chr19:54783502-54783200303LIRB2_HUMAN119-2201021A:97-198 (gaps)102
1.7ENST000003917497ENSE00001758109chr19:54782963-54782667297LIRB2_HUMAN220-3191001A:198-1981
1.8aENST000003917498aENSE00001754977chr19:54782416-54782114303LIRB2_HUMAN319-4201020--
1.9ENST000003917499ENSE00000856180chr19:54781793-5478174351LIRB2_HUMAN420-437180--
1.10aENST0000039174910aENSE00001747652chr19:54781454-5478140451LIRB2_HUMAN437-454180--
1.10eENST0000039174910eENSE00001749680chr19:54780783-54780661123LIRB2_HUMAN454-495420--
1.11ENST0000039174911ENSE00001639064chr19:54780310-5478023576LIRB2_HUMAN495-520260--
1.12aENST0000039174912aENSE00001780015chr19:54780155-5478011838LIRB2_HUMAN520-533140--
1.13ENST0000039174913ENSE00001639335chr19:54779857-5477980553LIRB2_HUMAN533-550180--
1.14cENST0000039174914cENSE00001817749chr19:54778683-54778320364LIRB2_HUMAN551-598480--

(-) 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:184
 aligned with LIRB2_HUMAN | Q8N423 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:195
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215     
          LIRB2_HUMAN    26 IPKPTLWAEPDSVITQGSPVTLSCQGSLEAQEYRLYREKKSASWITRIRPELVKNGQFHIPSITWEHTGRYGCQYYSRARWSELSDPLVLVMTGAYPKPTLSAQPSPVVTSGGRVTLQCESQVAFGGFILCKEGEEEHPQCLNSQPHARGSSRAIFSVGPVSPNRRWSHRCYGYDLNSPYVWSSPSDLLELLVPG 220
               SCOP domains d2gw5a1 A:3-97 automated matches                                                              d2gw5a2 A:98-198 automated matches                                                                    SCOP domains
               CATH domains 2gw5A01 A:3-96 Immunoglobulins                                                               2gw5A02 A:97-198 Immunoglobulins                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eee....eeeeee......eeeeeee.-----.ee.hhh.ee..eeee........eeeeeeeee..ee......eeeeee......eeeee..........eeeeeeeeeee.eeeeeee------.eee.......eeeeeeee.........eeeeeee..............ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: A:3-97 (gaps) UniProt: 24-119 [INCOMPLETE]                                    ----------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.6  PDB: A:97-198 (gaps) UniProt: 119-220                                                        Transcript 1 (2)
                 2gw5 A   3 IPKPTLWAEPDSVITQGSPVTLSCQGSLEAQEYRLYREK-----ITRIRPELVKNGQFHIPSITWEHTGRYGCQYYSRARWSELSDPLVLVMTGAYPKPTLSAQPSPVVTSGGRVTLQCESQVAFGGFILCKE------QCLNSQPHARGSSRAIFSVGPVSPNRRWSHRCYGYDLNSPYVWSSPSDLLELLVPG 198
                                    12        22        32        |-    |   52        62        72        82|       93       103       113       123       133  |    143       153       163       173       183       193     
                                                                 41    47                                 82|                                                 136    143                                                       
                                                                                                           84                                                                                                                  

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GW5)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LIRB2_HUMAN | Q8N423)
molecular function
    GO:0042288    MHC class I protein binding    Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0023029    MHC class Ib protein binding    Interacting selectively and non-covalently with major histocompatibility complex class Ib molecules.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0032396    inhibitory MHC class I receptor activity    Combining with a MHC class I protein complex to mediate signaling that inhibits activation of a lymphocyte.
    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:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0002774    Fc receptor mediated inhibitory signaling pathway    A series of molecular signals generated as a consequence of the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of inhibiting an immune effector process contributing to an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    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:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002767    immune response-inhibiting cell surface receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell capable of inhibiting an immune response.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0002578    negative regulation of antigen processing and presentation    Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation.
    GO:0051926    negative regulation of calcium ion transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050777    negative regulation of immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0002666    positive regulation of T cell tolerance induction    Any process that activates or increases the frequency, rate, or extent of T cell tolerance induction.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0045591    positive regulation of regulatory T cell differentiation    Any process that activates or increases the frequency, rate or extent of differentiation of regulatory T cells.
    GO:0002645    positive regulation of tolerance induction    Any process that activates or increases the frequency, rate, or extent of tolerance induction.
    GO:2001198    regulation of dendritic cell differentiation    Any process that modulates the frequency, rate or extent of dendritic cell differentiation.
    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: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.
cellular component
    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: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: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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        LIRB2_HUMAN | Q8N4232dyp 4lla

(-) Related Entries Specified in the PDB File

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