2D6M - JenaLib

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Title :   CRYSTAL STRUCTURE OF MOUSE GALECTIN-9 N-TERMINAL CRD IN COMPLEX WITH LACTOSE

Authors :   M. Nagae, N. Nishi, T. Nakamura, S. Wakatsuki, R. Kato

Date :   14 Nov 05 (Deposition) - 26 Sep 06 (Release) - 13 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Beta Sandwich, Carbohydrate Binding Protein, Galectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nagae, N. Nishi, T. Murata, T. Usui, T. Nakamura, S. Wakatsuki, R. Kato
Crystal Structure Of The Galectin-9 N-Terminal Carbohydrate Recognition Domain From Mus Musculus Reveals The Basic Mechanism Of Carbohydrate Recognition
J. Biol. Chem. V. 281 35884 2006
PubMed-ID: 16990264 | Reference-DOI: 10.1074/JBC.M606648200
(for further references see the PDB file header)

Molecule 1 - LECTIN, GALACTOSE BINDING, SOLUBLE 9
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN(RESIDUES 1-157)
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	GALECTIN-9

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	LBT	2	Ligand/Ion	ALPHA-LACTOSE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	LBT	2	Ligand/Ion	ALPHA-LACTOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LBT	1	Ligand/Ion	ALPHA-LACTOSE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	LBT	1	Ligand/Ion	ALPHA-LACTOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1451 , HIS B:60 , ASN B:62 , ARG B:64 , ASN B:74 , GLU B:84 , ARG B:86 , HOH B:1327 , HOH B:1329 , HOH B:1347 , HOH B:1350 , HOH B:1395 , HOH B:1521	BINDING SITE FOR RESIDUE LBT B 1300
2	AC2	SOFTWARE	HIS A:60 , ASN A:62 , ARG A:64 , ASN A:74 , TRP A:81 , GLU A:84 , ARG A:86 , HOH A:1428 , HOH A:1469 , HOH A:1481 , HOH A:1508 , HOH A:1526 , HOH A:1570 , HOH A:1605 , HOH A:1606 , HOH A:1612 , HOH A:1624	BINDING SITE FOR RESIDUE LBT A 1400

(no "SS Bond" information available for 2D6M)

Asymmetric Unit

No.	Residues
1	Ile A:15	-	Pro A:16
2	Ile B:15	-	Pro B:16

(no "SAP(SNP)/Variant" information available for 2D6M)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_MOUSE	17-147 225-353	2	A:17-147 B:17-147 -

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_MOUSE	17-147 225-353	2	A:17-147 B:17-147 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_MOUSE	17-147 225-353	1	A:17-147 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG9_MOUSE	17-147 225-353	1	- B:17-147 -

(no "Exon" information available for 2D6M)

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:151
 aligned with LEG9_MOUSE | O08573 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:151
                              1                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148 
           LEG9_MOUSE     - --MALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQNS 149
               SCOP domains d2d6ma_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....eeee.........eeeeeeee......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------GALECTIN  PDB: A:17-147 UniProt: 17-147                                                                                            -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d6m A  -1 GSMALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQTQ 149
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with LEG9_MOUSE | O08573 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:151
                              1                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148 
           LEG9_MOUSE     - --MALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQNS 149
               SCOP domains d2d6mb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....eeee........eeeeeeeee......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------GALECTIN  PDB: B:17-147 UniProt: 17-147                                                                                            -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d6m B  -1 GSMALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQTQ 149
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

Mouse (Mus musculus) [TaxId: 10090] (10)

1a	d2d6ma_	A:
1b	d2d6mb_	B:

(no "CATH Domain" information available for 2D6M)

(no "Pfam Domain" information available for 2D6M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LEG9_MOUSE | O08573)

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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0016936	galactoside binding	Interacting selectively and non-covalently with any glycoside in which the sugar group is galactose.
	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:0043539	protein serine/threonine kinase activator activity	Binds to and increases the activity of a protein serine/threonine kinase.
	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: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: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: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:0045185	maintenance of protein location	Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away.
	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: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:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	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:1902714	negative regulation of interferon-gamma secretion	Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion.
	GO:0032815	negative regulation of natural killer cell activation	Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation.
	GO:0043322	negative regulation of natural killer cell degranulation	Any process that stops, prevents, or reduces the rate of natural killer cell degranulation.
	GO:2000406	positive regulation of T cell migration	Any process that activates or increases the frequency, rate or extent of T cell migration.
	GO:0032722	positive regulation of chemokine production	Any process that activates or increases the frequency, rate, or extent of chemokine production.
	GO:0001819	positive regulation of cytokine production	Any process that activates or increases the frequency, rate or extent of production of a cytokine.
	GO:1900426	positive regulation of defense response to bacterium	Any process that activates or increases the frequency, rate or extent of defense response to bacterium.
	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:0045089	positive regulation of innate immune response	Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
	GO:0032732	positive regulation of interleukin-1 production	Any process that activates or increases the frequency, rate, or extent of interleukin-1 production.
	GO:2001181	positive regulation of interleukin-10 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-10 secretion.
	GO:2000778	positive regulation of interleukin-6 secretion	Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
	GO:0043032	positive regulation of macrophage activation	Any process that stimulates, induces or increases the rate of macrophage activation.
	GO:0051353	positive regulation of oxidoreductase activity	Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
	GO:0010862	positive regulation of pathway-restricted SMAD protein phosphorylation	Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0071902	positive regulation of protein serine/threonine kinase activity	Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
	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:2000679	positive regulation of transcription regulatory region DNA binding	Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
	GO:0032760	positive regulation of tumor necrosis factor production	Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
	GO:0010819	regulation of T cell chemotaxis	Any process that modulates the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus.
	GO:0033081	regulation of T cell differentiation in thymus	Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus.
	GO:2000316	regulation of T-helper 17 type immune response	Any process that modulates the frequency, rate or extent of T-helper 17 type immune response.
	GO:0032823	regulation of natural killer cell differentiation	Any process that modulates the frequency, rate or extent of natural killer cell differentiation.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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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	2d6m
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	LEG9_MOUSE \| O08573	:	2d6k 2d6l 2d6n 2d6o 2d6p

2d6k	THE SAME PROTEIN(CRYSTAL FORM1)
2d6l	THE SAME PROTEIN(CRYSTAL FORM2)
2d6n	THE SAME PROTEIN(N-ACETYLLACTOSAMINE COMPLEX)
2d6o	THE SAME PROTEIN(LN2 COMPLEX)
2d6p	THE SAME PROTEIN(T-ANTIGEN COMPLEX)

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