3AYC - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GALECTIN-3 CRD DOMIAN COMPLEXED WITH GM1 PENTASACCHARIDE

Authors :   C. F. Bian, D. F. Li, D. C. Wang

Date :   04 May 11 (Deposition) - 12 Oct 11 (Release) - 12 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Rossmann Fold, A Beta-Galactose-Binding Protein, Beta-Galactosides, Cell-Surface, Nuclear, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. F. Bian, Y. Zhang, H. Sun, D. F. Li, D. C. Wang
Structural Basis For Distinct Binding Properties Of The Human Galectins To Thomsen-Friedenreich Antigen
Plos One V. 6 25007 2011
PubMed-ID: 21949831 | Reference-DOI: 10.1371/JOURNAL.PONE.0025007

Molecule 1 - GALECTIN-3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, UNP RESIDUES 117-250
	Gene	:	LGALS3, MAC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAL-3, 35 KDA LECTIN, CARBOHYDRATE-BINDING PROTEIN 35, CBP 35, GALACTOSE-SPECIFIC LECTIN 3, GALACTOSIDE-BINDING PROTEIN, GALBP, IGE-BINDING PROTEIN, L-31, LAMININ-BINDING PROTEIN, LECTIN L-29, MAC- 2 ANTIGEN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 13)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	1	Ligand/Ion	GLYCEROL
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	1	Ligand/Ion	O-SIALIC ACID
7	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	BGC	-1	Ligand/Ion	BETA-D-GLUCOSE
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	1	Ligand/Ion	GLYCEROL
5	NGA	-1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	-1	Ligand/Ion	O-SIALIC ACID
7	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (6, 10)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	-1	Ligand/Ion	GLYCEROL
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	1	Ligand/Ion	O-SIALIC ACID
7	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:158 , ASN A:160 , ARG A:162 , ASN A:174 , GLU A:184 , HOH A:259 , HOH A:292 , HOH A:454	BINDING SITE FOR RESIDUE GOL A 1
02	AC2	SOFTWARE	HOH A:106 , HOH A:109 , HOH A:112 , ARG A:151 , ARG A:224 , VAL A:225 , LYS A:226 , LYS A:227 , HOH B:376	BINDING SITE FOR RESIDUE SO4 A 4
03	AC3	SOFTWARE	ASN A:222 , SO4 B:3 , HOH B:29 , TYR B:247 , HOH B:328 , HOH B:329	BINDING SITE FOR RESIDUE BME A 251
04	AC4	SOFTWARE	HOH B:57 , HOH B:76 , HIS B:158 , ASN B:160 , ARG B:162 , ASN B:174 , GLU B:184 , NGA B:299 , HOH B:327 , HOH B:363 , HOH B:375 , HOH B:401	BINDING SITE FOR RESIDUE GAL B 298
05	AC5	SOFTWARE	ARG B:162 , GLU B:184 , ARG B:186 , HOH B:297 , GAL B:298 , GAL B:300 , SIA B:302 , HOH B:344	BINDING SITE FOR RESIDUE NGA B 299
06	AC6	SOFTWARE	ASN A:166 , NGA B:299 , BGC B:301 , SIA B:302	BINDING SITE FOR RESIDUE GAL B 300
07	AC7	SOFTWARE	ASN A:164 , GLU A:165 , ASN A:166 , ASN B:166 , HOH B:253 , HOH B:293 , HOH B:294 , GAL B:300 , HOH B:433	BINDING SITE FOR RESIDUE BGC B 301
08	AC8	SOFTWARE	ASN A:167 , HOH B:44 , HOH B:92 , HOH B:101 , VAL B:189 , ALA B:216 , HIS B:217 , HOH B:292 , NGA B:299 , GAL B:300 , HOH B:313 , HOH B:327 , HOH B:368 , HOH B:450	BINDING SITE FOR RESIDUE SIA B 302
09	AC9	SOFTWARE	THR A:248 , HOH A:289 , HOH B:33 , ARG B:183 , ARG B:224 , HOH B:355 , HOH B:374 , HOH B:414 , HOH B:422	BINDING SITE FOR RESIDUE SO4 B 1
10	BC1	SOFTWARE	HOH A:252 , ARG B:151 , ARG B:224 , VAL B:225 , LYS B:226 , LYS B:227 , HOH B:259 , HOH B:268 , HOH B:305 , HOH B:385	BINDING SITE FOR RESIDUE SO4 B 2
11	BC2	SOFTWARE	ARG A:183 , ARG A:224 , BME A:251 , HOH A:307 , HOH B:69 , THR B:248 , HOH B:328 , HOH B:329 , HOH B:331 , HOH B:346	BINDING SITE FOR RESIDUE SO4 B 3
12	BC3	SOFTWARE	LYS A:226 , HOH B:62 , LYS B:199 , GLN B:201 , HOH B:376	BINDING SITE FOR RESIDUE SO4 B 5
13	BC4	SOFTWARE	HIS B:217 , LEU B:219 , GLN B:220	BINDING SITE FOR RESIDUE BME B 251

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049768	R	183	K	LEG3_HUMAN	Polymorphism	10148371	A/B	R	183	K

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049768	R	183	K	LEG3_HUMAN	Polymorphism	10148371	A	R	183	K

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049768	R	183	K	LEG3_HUMAN	Polymorphism	10148371	B	R	183	K

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG3_HUMAN	118-248	2	A:118-248 B:118-248

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.	LEG3_HUMAN	118-248	1	A:118-248 -

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.	LEG3_HUMAN	118-248	1	- B:118-248

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000254301	1	ENSE00001536507	chr14:55595872-55596018	147	LEG3_HUMAN	-	0	0	-	-
1.2b	ENST00000254301	2b	ENSE00001536493	chr14:55604088-55604109	22	LEG3_HUMAN	1-6	6	0	-	-
1.2c	ENST00000254301	2c	ENSE00001002799	chr14:55604763-55605086	324	LEG3_HUMAN	7-114	108	0	-	-
1.3	ENST00000254301	3	ENSE00001757559	chr14:55606993-55607081	89	LEG3_HUMAN	115-144	30	2	A:116-144 B:116-144	29 29
1.4	ENST00000254301	4	ENSE00001682369	chr14:55609302-55609467	166	LEG3_HUMAN	144-199	56	2	A:144-199 B:144-199	56 56
1.5b	ENST00000254301	5b	ENSE00001786819	chr14:55611834-55612147	314	LEG3_HUMAN	200-250	51	2	A:200-250 B:200-250	51 51

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:135
 aligned with LEG3_HUMAN | P17931 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:135
                                   125       135       145       155       165       175       185       195       205       215       225       235       245     
           LEG3_HUMAN   116 VPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
               SCOP domains d3ayca_ A: Galectin-3 CRD                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeeee......eeeeeee..eeeeeeeee.......eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------K------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: A:118-248 UniProt: 118-248                                                                                          -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:116-144     -------------------------------------------------------Exon 1.5b  PDB: A:200-250 UniProt: 200-250          Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.4  PDB: A:144-199 UniProt: 144-199               --------------------------------------------------- Transcript 1 (2)
                 3ayc A 116 MPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
                                   125       135       145       155       165       175       185       195       205       215       225       235       245

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with LEG3_HUMAN | P17931 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:135
                                   125       135       145       155       165       175       185       195       205       215       225       235       245     
           LEG3_HUMAN   116 VPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
               SCOP domains d3aycb_ B: Galectin-3 CRD                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeeee......eeeeeee..eeeeeeeee.......eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------K------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: B:118-248 UniProt: 118-248                                                                                          -- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:116-144     -------------------------------------------------------Exon 1.5b  PDB: B:200-250 UniProt: 200-250          Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.4  PDB: B:144-199 UniProt: 144-199               --------------------------------------------------- Transcript 1 (2)
                 3ayc B 116 MPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
                                   125       135       145       155       165       175       185       195       205       215       225       235       245

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(

)

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: Galectin (animal S-lectin) (75)

Protein domain: Galectin-3 CRD (22)

Human (Homo sapiens) [TaxId: 9606] (22)

1a	d3ayca_	A:
1b	d3aycb_	B:

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

(no "Pfam Domain" information available for 3AYC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LEG3_HUMAN | P17931)

molecular function
	GO:0019863	IgE binding	Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype.
	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:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	GO:0043236	laminin binding	Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
	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).
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0048245	eosinophil chemotaxis	The movement of an eosinophil in response to an external stimulus.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0048246	macrophage chemotaxis	The movement of a macrophage in response to an external stimulus.
	GO:0002548	monocyte chemotaxis	The movement of a monocyte in response to an external stimulus.
	GO:0071674	mononuclear cell migration	The movement of a mononuclear cell within or between different tissues and organs of the body.
	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:0050860	negative regulation of T cell receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045806	negative regulation of endocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.
	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
	GO:2000521	negative regulation of immunological synapse formation	Any process that stops, prevents or reduces the frequency, rate or extent of immunological synapse formation.
	GO:0030593	neutrophil chemotaxis	The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:0090280	positive regulation of calcium ion import	Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
	GO:2001200	positive regulation of dendritic cell differentiation	Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
	GO:0071677	positive regulation of mononuclear cell migration	Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.
	GO:0070232	regulation of T cell apoptotic process	Any process that modulates the occurrence or rate of T cell death by apoptotic process.
	GO:0042129	regulation of T cell proliferation	Any process that modulates the frequency, rate or extent of T cell proliferation.
	GO:1902041	regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0001772	immunological synapse	An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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.
	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.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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	LEG3_HUMAN \| P17931
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (3, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (39, 39)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File