1UGN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LIR1.02, ONE OF THE ALLELES OF LIR1

Authors :   M. Shiroishi, L. Rasubala, K. Kuroki, K. Amano, N. Tsuchiya, K. Tokunaga, D. Kohda, K. Maenaka

Date :   17 Jun 03 (Deposition) - 10 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Immunoglobulin-Like Folds, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kuroki, N. Tsuchiya, M. Shiroishi, L. Rasubala, Y. Yamashita, K. Matsuta, T. Fukazawa, M. Kusaoi, Y. Murakami, M. Takiguchi, T. Juji, H. Hashimoto, D. Kohda, K. Maenaka, K. Tokunaga
Extensive Polymorphisms Of Lilrb1 (Ilt2, Lir1) And Their Association With Hla-Drb1 Shared Epitope Negative Rheumatoid Arthritis.
Hum. Mol. Genet. V. 14 2469 2005
PubMed-ID: 16014635 | Reference-DOI: 10.1093/HMG/DDI247
(for further references see the PDB file header)

Molecule 1 - LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 1
	Chains	:	A
	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 (DOMAIN1 AND 2)
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LIR1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1UGN)

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:75
2	A:122	-	A:174
3	A:134	-	A:144

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_016993	L	68	P	LIRB1_HUMAN	Polymorphism	1061679	A	P	45	P
2	UniProt	VAR_049888	A	93	T	LIRB1_HUMAN	Polymorphism	12460501	A	T	70	T
3	UniProt	VAR_016994	I	142	T	LIRB1_HUMAN	Polymorphism	1061680	A	T	119	T
4	UniProt	VAR_016995	S	155	I	LIRB1_HUMAN	Polymorphism	1061681	A	I	132	I

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

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

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000396331	3	ENSE00001524582	chr19:55128612-55128803	192	LIRB1_HUMAN	-	0	0	-	-
1.4d	ENST00000396331	4d	ENSE00001524607	chr19:55141968-55142084	117	LIRB1_HUMAN	-	0	0	-	-
1.4f	ENST00000396331	4f	ENSE00001772529	chr19:55142477-55142558	82	LIRB1_HUMAN	1-12	12	0	-	-
1.5b	ENST00000396331	5b	ENSE00001770130	chr19:55142722-55142757	36	LIRB1_HUMAN	12-24	13	1	A:1-1	1
1.6	ENST00000396331	6	ENSE00001739075	chr19:55142951-55143238	288	LIRB1_HUMAN	24-120	97	1	A:1-97	97
1.7b	ENST00000396331	7b	ENSE00001642167	chr19:55143386-55143688	303	LIRB1_HUMAN	120-221	102	1	A:97-198 (gaps)	102
1.8	ENST00000396331	8	ENSE00001697649	chr19:55143915-55144211	297	LIRB1_HUMAN	221-320	100	1	A:198-198	1
1.9a	ENST00000396331	9a	ENSE00001653351	chr19:55144467-55144769	303	LIRB1_HUMAN	320-421	102	0	-	-
1.10	ENST00000396331	10	ENSE00000726302	chr19:55145089-55145139	51	LIRB1_HUMAN	421-438	18	0	-	-
1.11c	ENST00000396331	11c	ENSE00001653883	chr19:55145425-55145472	48	LIRB1_HUMAN	438-454	17	0	-	-
1.12d	ENST00000396331	12d	ENSE00001626275	chr19:55146092-55146214	123	LIRB1_HUMAN	454-495	42	0	-	-
1.13b	ENST00000396331	13b	ENSE00001769852	chr19:55146555-55146630	76	LIRB1_HUMAN	495-520	26	0	-	-
1.14	ENST00000396331	14	ENSE00001684637	chr19:55146710-55146747	38	LIRB1_HUMAN	520-533	14	0	-	-
1.15a	ENST00000396331	15a	ENSE00001649211	chr19:55147008-55147060	53	LIRB1_HUMAN	533-550	18	0	-	-
1.15f	ENST00000396331	15f	ENSE00001802166	chr19:55147948-55148103	156	LIRB1_HUMAN	551-602	52	0	-	-
1.16d	ENST00000396331	16d	ENSE00001266337	chr19:55148183-55148979	797	LIRB1_HUMAN	603-650	48	0	-	-

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:186
 aligned with LIRB1_HUMAN | Q8NHL6 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:198
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
          LIRB1_HUMAN    24 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTALWITRIPQELVKKGQFPIPSITWEHAGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVILQCDSQVAFDGFSLCKEGEDEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVLG 221
               SCOP domains -d1ugna1 A:2-97 Ligand binding domain of lir-1 (ilt2)                                            d1ugna2 A:98-195 Ligand binding domain       of li      r-1 (ilt2)                                --- SCOP domains
               CATH domains -1ugnA01 A:2-96 Immunoglobulins                                                                 1ugnA02 A:97-198 Immunoglobulins                                                                       CATH domains
               Pfam domains ----Ig_2-1ugnA01 A:5-95                                                                        -----Ig_3-1ugnA02 A:101-180                                                          ------------------ Pfam domains
         Sec.struct. author ......eeeee...eee....eeeeee.......eeeee....hhhhhh.hhhhhh..eeee...hhhhheeeeeeeee...ee......eeeeee......eeeee...eee....eeeeee......eeeeeee------.eee.------..eeeeee........eeeeeeee......ee......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------P------------------------T------------------------------------------------T------------I------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------------------------------------Exon 1.7b  PDB: A:97-198 (gaps) UniProt: 120-221                                                       Transcript 1 (1)
           Transcript 1 (2) Exon 1.6  PDB: A:1-97 UniProt: 24-120                                                            ----------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 1ugn A   1 GHLPKPTLWAEPGSVITQGSPVTLRCQGGQETQEYRLYREKKTAPWITRIPQELVKKGQFPIPSITWEHTGRYRCYYGSDTAGRSESSDPLELVVTGAYIKPTLSAQPSPVVNSGGNVTLQCDSQVAFDGFILCKE------QCLNS------SSRAIFSVGPVSPSRRWWYRCYAYDSNSPYEWSLPSDLLELLVLG 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |   -  |   |  -   |   160       170       180       190        
                                                                                                                                                                 136    143 147    154

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: I set domains (152)

Protein domain: Ligand binding domain of lir-1 (ilt2) (5)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d1ugna1	A:2-97
1b	d1ugna2	A:98-195

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	1ugnA02	A:97-198
1b	1ugnA01	A:2-96

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: Ig_2 (52)

Homo sapiens (Human) (39)

Ig_2-1ugnA01

A:5-95

Family: Ig_3 (11)

Homo sapiens (Human) (9)

Ig_3-1ugnA02

A:101-180

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 1ugn)

	Cis Peptide Bonds
		Gln A:107 - Pro A:108	[ RasMol ]
		Glu A:11 - Pro A:12	[ RasMol ]
		Gly A:162 - Pro A:163	[ RasMol ]

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	1ugn
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	LIRB1_HUMAN \| Q8NHL6	:	1g0x 1p7q 1ufu 1vdg 3d2u 4ll9 4no0 5knm

1g0x	THE STRUCTURE OF LIR1.03 FROM THE DIFFERENT FORM OF CRYSTAL FROM THIS CRYSTAL.
1ufu	THE STRUCTURE OF LIR1.03 FROM THE SAME FORM OF CRYSTAL AS THIS CRYSTAL.

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