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(-) Description

Title :  CRYSTAL STRUCTURE OF LIR1.01, ONE OF THE ALLELES OF LIR1
 
Authors :  M. Shiroishi, L. Rasubala, K. Kuroki, K. Amano, N. Tsuchiya, K. Tokunaga, D. Kohda, K. Maenaka
Date :  22 Mar 04  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin-Like, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Shiroishi, L. Rasubala, K. Kuroki, K. Amano, N. Tsuchiya, K. Tokunaga, D. Kohda, K. Maenaka
Crystal Structure Of Lir1. 03, One Of The Alleles Of Lir1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR SUBFAMILY B MEMBER 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGMT7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN (DOMAIN 1 AND 2)
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 1, LIR-1, IMMUNOGLOBULIN- LIKE TRANSCRIPT 2, ILT-2, MONOCYTE/MACROPHAGE IMMUNOGLOBULIN-LIKE RECEPTOR 7, MIR-7, CD85J ANTIGEN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VDG)

(-) Sites  (0, 0)

(no "Site" information available for 1VDG)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:75
2A:122 -A:174
3A:134 -A:144
4B:26 -B:75
5B:122 -B:174
6B:134 -B:144

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:11 -Pro A:12
2Gln A:107 -Pro A:108
3Gly A:162 -Pro A:163
4Glu B:11 -Pro B:12
5Gln B:107 -Pro B:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016993L68PLIRB1_HUMANPolymorphism1061679A/BL45P
2UniProtVAR_049888A93TLIRB1_HUMANPolymorphism12460501A/BA70T
3UniProtVAR_016994I142TLIRB1_HUMANPolymorphism1061680A/BI119T
4UniProtVAR_016995S155ILIRB1_HUMANPolymorphism1061681A/BS132I
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VDG)

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003963313ENSE00001524582chr19:55128612-55128803192LIRB1_HUMAN-00--
1.4dENST000003963314dENSE00001524607chr19:55141968-55142084117LIRB1_HUMAN-00--
1.4fENST000003963314fENSE00001772529chr19:55142477-5514255882LIRB1_HUMAN1-12120--
1.5bENST000003963315bENSE00001770130chr19:55142722-5514275736LIRB1_HUMAN12-24132A:1-1
B:1-1		1
1
1.6ENST000003963316ENSE00001739075chr19:55142951-55143238288LIRB1_HUMAN24-120972A:1-97 (gaps)
B:1-97 (gaps)		97
97
1.7bENST000003963317bENSE00001642167chr19:55143386-55143688303LIRB1_HUMAN120-2211022A:97-197 (gaps)
B:97-197 (gaps)		101
101
1.8ENST000003963318ENSE00001697649chr19:55143915-55144211297LIRB1_HUMAN221-3201000--
1.9aENST000003963319aENSE00001653351chr19:55144467-55144769303LIRB1_HUMAN320-4211020--
1.10ENST0000039633110ENSE00000726302chr19:55145089-5514513951LIRB1_HUMAN421-438180--
1.11cENST0000039633111cENSE00001653883chr19:55145425-5514547248LIRB1_HUMAN438-454170--
1.12dENST0000039633112dENSE00001626275chr19:55146092-55146214123LIRB1_HUMAN454-495420--
1.13bENST0000039633113bENSE00001769852chr19:55146555-5514663076LIRB1_HUMAN495-520260--
1.14ENST0000039633114ENSE00001684637chr19:55146710-5514674738LIRB1_HUMAN520-533140--
1.15aENST0000039633115aENSE00001649211chr19:55147008-5514706053LIRB1_HUMAN533-550180--
1.15fENST0000039633115fENSE00001802166chr19:55147948-55148103156LIRB1_HUMAN551-602520--
1.16dENST0000039633116dENSE00001266337chr19:55148183-55148979797LIRB1_HUMAN603-650480--

(-) 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:187
 aligned with LIRB1_HUMAN | Q8NHL6 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:197
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
          LIRB1_HUMAN    24 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVL 220
               SCOP domains d1vdga1 A:1-97 automated matches                                                                 d1vdga2 A:98-197 automated matches                                                                   SCOP domains
               CATH domains -1vdgA01 A:2-96 Immunoglobulins                                                                 1vdgA02 A:97-197 Immunoglobulins                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...eee....eeeeee.......eeeee......hhhhhhhhhhhh.eeee...hhhhheeeeeee.----........eeeeee......eeeee...eee....eeeeee......eeeeee.------.eeee........eeeeee.........eeeeeee......ee......ee.eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------P------------------------T------------------------------------------------T------------I----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------------------------------------Exon 1.7b  PDB: A:97-197 (gaps) UniProt: 120-221 [INCOMPLETE]                                         Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: A:1-97 (gaps) UniProt: 24-120                                                     ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1vdg A   1 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYG----GRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKE------QCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVL 197
                                    10        20        30        40        50        60        70       | -  |     90       100       110       120       130     |   -  |    150       160       170       180       190       
                                                                                                        78   83                                                  136    143                                                      


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with LIRB1_HUMAN | Q8NHL6 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:197
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
          LIRB1_HUMAN    24 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVL 220
               SCOP domains d1vdgb1 B:1-97 automated matches                                                                 d1vdgb2 B:98-197 automated matches                                                                   SCOP domains
               CATH domains -1vdgB01 B:2-96 Immunoglobulins                                                                 1vdgB02 B:97-197 Immunoglobulins                                                                      CATH domains
           Pfam domains (1) ----Ig_2-1vdgB01 B:5-95                                                                        -----Ig_3-1vdgB03 B:101-180                                                          ----------------- Pfam domains (1)
           Pfam domains (2) ----Ig_2-1vdgB02 B:5-95                                                                        -----Ig_3-1vdgB04 B:101-180                                                          ----------------- Pfam domains (2)
         Sec.struct. author ......eeeee...eee....eeeeee.......eeeee....hhhhhhhhhhhhh..eeee...hhhhheeeeeee...-.........eeeeee......eeeee...eee....eeeeee......eeeeee.------.eeee..--....eeeeee......-..eeeeeee..............ee.eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------P------------------------T------------------------------------------------T------------I----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------------------------------------Exon 1.7b  PDB: B:97-197 (gaps) UniProt: 120-221 [INCOMPLETE]                                         Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: B:1-97 (gaps) UniProt: 24-120                                                     ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1vdg B   1 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSD-AGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKE------QCLNSQP--RGSSRAIFSVGPVSPS-RWWYRCYAYDSNSPYEWSLPSDLLELLVL 197
                                    10        20        30        40        50        60        70        80 |      90       100       110       120       130     |   -  |     |- |     160      |170       180       190       
                                                                                                          80 |                                                   136    143   149  |            167 |                            
                                                                                                            82                                                                   152              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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (55, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LIRB1_HUMAN | Q8NHL6)
molecular function
    GO:0030107    HLA-A specific inhibitory MHC class I receptor activity    Combining with a MHC class I molecule of the HLA-A subclass to mediate signaling that inhibits activation of a lymphocyte.
    GO:0030109    HLA-B specific inhibitory MHC class I receptor activity    Combining with a MHC class I molecule of the HLA-B subclass to mediate signaling that inhibits activation of a lymphocyte.
    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:0032393    MHC class I receptor activity    Combining with an MHC class I protein complex to initiate a change in cellular activity. Class I here refers to classical class I molecules.
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008157    protein phosphatase 1 binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 1.
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:0002309    T cell proliferation involved in immune response    The expansion of a T cell population by cell division as part of an immune response.
    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: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:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0097028    dendritic cell differentiation    The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
    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:0032609    interferon-gamma production    The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
    GO:0072643    interferon-gamma secretion    The regulated release of interferon-gamma from a cell.
    GO:2001186    negative regulation of CD8-positive, alpha-beta T cell activation    Any process that stops, prevents or reduces the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.
    GO:2001189    negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell    Any process that stops, prevents or reduces the frequency, rate or extent of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell.
    GO:0001915    negative regulation of T cell mediated cytotoxicity    Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0046636    negative regulation of alpha-beta T cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell activation.
    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:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0002740    negative regulation of cytokine secretion involved in immune response    Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine secretion contributing to an immune response.
    GO:2000669    negative regulation of dendritic cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell apoptotic process.
    GO:2001199    negative regulation of dendritic cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation.
    GO:0045806    negative regulation of endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.
    GO:0035548    negative regulation of interferon-beta secretion    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-beta secretion.
    GO:0045077    negative regulation of interferon-gamma biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:2001180    negative regulation of interleukin-10 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-10 secretion.
    GO:2001183    negative regulation of interleukin-12 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-12 secretion.
    GO:0032945    negative regulation of mononuclear cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation.
    GO:0045953    negative regulation of natural killer cell mediated cytotoxicity    Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity.
    GO:2001205    negative regulation of osteoclast development    Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development.
    GO:0014063    negative regulation of serotonin secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin.
    GO:2001202    negative regulation of transforming growth factor-beta secretion    Any process that stops, prevents or reduces the frequency, rate or extent of transforming growth factor-beta secretion.
    GO:0042536    negative regulation of tumor necrosis factor biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0045919    positive regulation of cytolysis    Any process that activates or increases the frequency, rate or extent of cytolysis.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:2001193    positive regulation of gamma-delta T cell activation involved in immune response    Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation involved in immune response.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    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:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        LIRB1_HUMAN | Q8NHL6: 1g0x 1p7q 1ufu 1ugn 3d2u 4ll9 4no0 5knm

(-) Related Entries Specified in the PDB File

1g0x CRYSTAL STRUCTURE OF LIR1.03 (SPACE GROUP P41212)
1ufu CRYSTAL STRUCTURE OF LIR1.03 (SPACE GROUP P21212)
1ugn CRYSTAL STRUCTURE OF LIR1.02