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Title :   N-DOMAIN OF HUMAN ADHESION/GROWTH-REGULATORY GALECTIN-9 IN COMPLEX WITH LACTOSE

Authors :   F. M. Ruiz, A. Romero

Date :   12 Feb 10 (Deposition) - 05 May 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.69

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Mainly Beta, Alternative Splicing, Cytoplasm, Lectin, Polymorphism, Secreted, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Solis, M. J. Mate, M. Lohr, J. P. Ribeiro, L. Lopez-Merino, S. Andre, E. Buzamet, F. J. Canada, H. Kaltner, M. Lensch, F. M. Ruiz, G. Haroske, U. Wollina, M. Kloor, J. Kopitz, J. L. Saiz, M. Menendez, J. Jimenez-Barbero, A. Romero, H. J. Gabius
N-Domain Of Human Adhesion/Growth-Regulatory Galectin-9: Preference For Distinct Conformers And Non-Sialylated N-Glycans And Detection Of Ligand-Induced Structural Changes In Crystal And Solution.
Int. J. Biochem. Cell Biol. V. 42 1019 2010
PubMed-ID: 20227520 | Reference-DOI: 10.1016/J.BIOCEL.2010.03.007

Molecule 1 - GALECTIN-9
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-12A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 6-148
	Gene	:	LGALS9
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAL-9, HOM-HD-21, ECALECTIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	LAT	1	Ligand/Ion	BETA-LACTOSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LAT	1	Ligand/Ion	BETA-LACTOSE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	LAT	2	Ligand/Ion	BETA-LACTOSE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:27 , GLY A:28 , ARG A:44 , HIS A:61 , ASN A:63 , ARG A:65 , ASN A:75 , TRP A:82 , GLU A:85 , ARG A:87 , GLN A:106	BINDING SITE FOR RESIDUE LAT A 1

(no "SS Bond" information available for 3LSE)

(no "Cis Peptide Bond" information available for 3LSE)

(no "SAP(SNP)/Variant" information available for 3LSE)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_HUMAN	17-148 227-355	1	A:17-148 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_HUMAN	17-148 227-355	1	A:17-148 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_HUMAN	17-148 227-355	2	A:17-148 -

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000395473	1a	ENSE00002165006	chr17:25956824-25958330	1507	LEG9_HUMAN	1-13	13	1	A:6-13	8
1.2	ENST00000395473	2	ENSE00001721697	chr17:25965289-25965380	92	LEG9_HUMAN	14-44	31	1	A:14-44	31
1.3a	ENST00000395473	3a	ENSE00001630948	chr17:25967598-25967799	202	LEG9_HUMAN	44-111	68	1	A:44-111	68
1.5	ENST00000395473	5	ENSE00001709088	chr17:25969264-25969374	111	LEG9_HUMAN	112-148	37	1	A:112-148	37
1.6	ENST00000395473	6	ENSE00001727464	chr17:25970551-25970646	96	LEG9_HUMAN	149-180	32	0	-	-
1.7c	ENST00000395473	7c	ENSE00001611626	chr17:25972340-25972375	36	LEG9_HUMAN	181-192	12	0	-	-
1.7d	ENST00000395473	7d	ENSE00001697897	chr17:25972887-25972937	51	LEG9_HUMAN	193-209	17	0	-	-
1.8	ENST00000395473	8	ENSE00001698891	chr17:25973573-25973614	42	LEG9_HUMAN	210-223	14	0	-	-
1.9a	ENST00000395473	9a	ENSE00001597519	chr17:25974056-25974144	89	LEG9_HUMAN	224-253	30	0	-	-
1.9c	ENST00000395473	9c	ENSE00001271333	chr17:25974296-25974458	163	LEG9_HUMAN	253-307	55	0	-	-
1.10f	ENST00000395473	10f	ENSE00001859656	chr17:25975862-25976586	725	LEG9_HUMAN	308-355	48	0	-	-

Asymmetric 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:143
 aligned with LEG9_HUMAN | O00182 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:143
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145   
           LEG9_HUMAN     6 SQAPYLSPAVPFSGTIQGGLQDGLQITVNGTVLSSSGTRFAVNFQTGFSGNDIAFHFNPRFEDGGYVVCNTRQNGSWGPEERKTHMPFQKGMPFDLCFLVQSSDFKVMVNGILFVQYFHRVPFHRVDTISVNGSVQLSYISFQ 148
               SCOP domains d3lsea_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Gal-bind_lectin-3lseA01 A:16-147                                                                                                    - Pfam domains
         Sec.struct. author ....ee.....eeee.........eeeeeeee.......eeeeee.......eeeeeeee.....eeeee.ee..ee...eee.........eeeeeeee...eeeeee...eeeeee.........eeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------GALECTIN  PDB: A:17-148 UniProt: 17-148                                                                                              PROSITE
           Transcript 1 (1) 1.1a    Exon 1.2  PDB: A:14-44         -------------------------------------------------------------------Exon 1.5  PDB: A:112-148              Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3a  PDB: A:44-111 UniProt: 44-111                            ------------------------------------- Transcript 1 (2)
                 3lse A   6 SQAPYLSPAVPFSGTIQGGLQDGLQITVNGTVLSSSGTRFAVNFQTGFSGNDIAFHFNPRFEDGGYVVCNTRQNGSWGPEERKTHMPFQKGMPFDLCFLVQSSDFKVMVNGILFVQYFHRVPFHRVDTISVNGSVQLSYISFQ 148
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: automated matches (133)

Protein domain: automated matches (133)

Human (Homo sapiens) [TaxId: 9606] (36)

d3lsea_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Gal-bind_lectin (60)

Homo sapiens (Human) (25)

Gal-bind_lectin-3lseA01

A:16-147

Asymmetric Unit(hide GO term definitions)

Chain A (LEG9_HUMAN | O00182)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0048030	disaccharide binding	Interacting selectively and non-covalently with any disaccharide. Disaccharides are sugars composed of two monosaccharide units.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0005534	galactose binding	Interacting selectively and non-covalently with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0070371	ERK1 and ERK2 cascade	An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0071346	cellular response to interferon-gamma	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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
	GO:0098586	cellular response to virus	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 stimulus from a virus.
	GO:0006935	chemotaxis	The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0007565	female pregnancy	The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
	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:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0060135	maternal process involved in female pregnancy	A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
	GO:0097029	mature conventional dendritic cell differentiation	The process in which antigen-activated dendritic cells acquire the specialized features of a mature conventional dendritic cell. Mature conventional dendritic cells upregulate the surface expression of MHC molecules, chemokine receptors and adhesion molecules, and increase the number of dendrites (cytoplasmic protrusions) in preparation for migration to lymphoid organs where they present antigen to T cells.
	GO:0002519	natural killer cell tolerance induction	Tolerance induction of natural killer cells.
	GO:2000562	negative regulation of CD4-positive, alpha-beta T cell proliferation	Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
	GO:0046007	negative regulation of activated T cell proliferation	Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
	GO:0032682	negative regulation of chemokine production	Any process that stops, prevents, or reduces the frequency, rate, or extent of chemokine production.
	GO:0010629	negative regulation of gene expression	Any process that decreases 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: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:0043305	negative regulation of mast cell degranulation	Any process that stops, prevents, or reduces the rate of mast cell degranulation.
	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:0032720	negative regulation of tumor necrosis factor production	Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
	GO:0038066	p38MAPK cascade	An intracellular protein kinase cascade containing at least a p38 MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0032834	positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response	Any process that activates or increases the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response.
	GO:2000563	positive regulation of CD4-positive, alpha-beta T cell proliferation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0042346	positive regulation of NF-kappaB import into nucleus	Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:2001190	positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	Any process that activates or increases 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:0070241	positive regulation of activated T cell autonomous cell death	Any process that activates or increases the frequency, rate or extent of activated T cell autonomous cell death.
	GO:2001269	positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
	GO:2000670	positive regulation of dendritic cell apoptotic process	Any process that activates or increases the frequency, rate or extent of dendritic cell apoptotic process.
	GO:2000510	positive regulation of dendritic cell chemotaxis	Any process that activates or increases the frequency, rate or extent of dendritic cell chemotaxis.
	GO:2001200	positive regulation of dendritic cell differentiation	Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
	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:1902715	positive regulation of interferon-gamma secretion	Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
	GO:0050718	positive regulation of interleukin-1 beta secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
	GO:2001181	positive regulation of interleukin-10 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-10 secretion.
	GO:2001184	positive regulation of interleukin-12 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-12 secretion.
	GO:2000667	positive regulation of interleukin-13 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-13 secretion.
	GO:0032753	positive regulation of interleukin-4 production	Any process that activates or increases the frequency, rate, or extent of interleukin-4 production.
	GO:2000778	positive regulation of interleukin-6 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
	GO:2000484	positive regulation of interleukin-8 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
	GO:0071639	positive regulation of monocyte chemotactic protein-1 production	Any process that activates or increases the frequency, rate, or extent of production of monocyte chemotactic protein-1.
	GO:0071636	positive regulation of transforming growth factor beta production	Any process that activates or increases the frequency, rate, or extent of production of transforming growth factor-beta.
	GO:1904469	positive regulation of tumor necrosis factor secretion	Any process that activates or increases the frequency, rate or extent of tumor necrosis factor secretion.
	GO:0046598	positive regulation of viral entry into host cell	Any process that activates or increases the frequency, rate or extent of the introduction of viral entry into the host cell.
	GO:0032673	regulation of interleukin-4 production	Any process that modulates the frequency, rate, or extent of interleukin-4 production.
	GO:0032674	regulation of interleukin-5 production	Any process that modulates the frequency, rate, or extent of interleukin-5 production.
	GO:1900744	regulation of p38MAPK cascade	Any process that modulates the frequency, rate or extent of p38MAPK cascade.
	GO:0070555	response to interleukin-1	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 an interleukin-1 stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (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:0034134	toll-like receptor 2 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 2.
	GO:0034142	toll-like receptor 4 signaling pathway	Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	LEG9_HUMAN \| O00182	:	2eak 2eal 2yy1 2zhk 2zhl 2zhm 2zhn 3lsd 3nv1 3nv2 3nv3 3nv4 3wlu 3wv6

3lsd	N-DOMAIN OF HUMAN ADHESION/GROWTH-REGULATORY GALECTIN-9

Description

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Ligands, Modified Residues, Ions (1, 1)

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