2YRO - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE C-TERMINAL GAL-BIND LECTIN PROTEIN FROM HUMAN GALECTIN-8

Authors :   T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   02 Apr 07 (Deposition) - 12 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Gal-Bind Lectin, Galectin, Sugar Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The C-Terminal Gal-Bind Lectin Protein From Human Galectin-8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GALECTIN-8
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050613-32
	Expression System Vector Type	:	PLASMID
	Fragment	:	GAL-BIND_LECTIN DOMAIN
	Gene	:	LGALS8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	GAL-8, PROSTATE CARCINOMA TUMOR ANTIGEN 1, PCTA-1, PO66 CARBOHYDRATE-BINDING PROTEIN, PO66-CBP


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YRO)

(no "Site" information available for 2YRO)

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

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Leu A:17	-	Pro A:18

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_063506	R	184	S	LEG8_HUMAN	Polymorphism	2243525	A	S	16	S

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG8_HUMAN	19-152 187-317	1	- A:19-149

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3c	ENST00000366584	3c	ENSE00001381502	chr1:236686899-236687361	463	LEG8_HUMAN	-	0	0	-	-
1.6a	ENST00000366584	6a	ENSE00002193374	chr1:236689268-236689415	148	LEG8_HUMAN	1-15	15	0	-	-
1.7b	ENST00000366584	7b	ENSE00002141991	chr1:236700797-236700885	89	LEG8_HUMAN	16-45	30	0	-	-
1.8b	ENST00000366584	8b	ENSE00000793501	chr1:236702179-236702389	211	LEG8_HUMAN	45-115	71	0	-	-
1.9b	ENST00000366584	9b	ENSE00000805377	chr1:236703864-236703983	120	LEG8_HUMAN	116-155	40	1	A:1-6	6
1.10e	ENST00000366584	10e	ENSE00000793503	chr1:236704954-236705010	57	LEG8_HUMAN	156-174	19	1	A:7-7	1
1.11c	ENST00000366584	11c	ENSE00001226656	chr1:236706061-236706087	27	LEG8_HUMAN	175-183	9	1	A:8-15	8
1.11r	ENST00000366584	11r	ENSE00002191373	chr1:236706860-236706948	89	LEG8_HUMAN	184-213	30	1	A:16-45	30
1.12c	ENST00000366584	12c	ENSE00000805385	chr1:236708050-236708215	166	LEG8_HUMAN	213-268	56	1	A:45-100	56
1.14j	ENST00000366584	14j	ENSE00001911385	chr1:236711312-236714310	2999	LEG8_HUMAN	269-317	49	1	A:101-149	49

NMR Structure

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:155
 aligned with LEG8_HUMAN | O00214 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:174
                                                                                                                                                                                                 317      
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       | -    
           LEG8_HUMAN   150 GFSFSSDLQSTQASSLELTEISRENVPKSGTPQLRLPFAARLNTPMGPGRTVVVKGEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPGMYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSW------   -
               SCOP domains d2yroa_                    A: automated matches                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------Gal-bind_lectin-2yroA01 A:18-148                                                                                                   ------- Pfam domains
         Sec.struct. author .......-------------------...........eeee.........eeeeeeee......eeeeee......eeeeee........eeeee.....................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------S------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GAL----------------------------------GALECTIN  PDB: A:19-149 UniProt: 187-317                                                                                           ------ PROSITE
           Transcript 1 (1) 1.9b  Exon 1.10e         1.11c    Exon 1.11r  PDB: A:16-45      -------------------------------------------------------Exon 1.14j  PDB: A:101-149 UniProt: 269-317      ------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.12c  PDB: A:45-100 UniProt: 213-268              ------------------------------------------------------- Transcript 1 (2)
                 2yro A   1 GSSGSSG-------------------PKSGTPQLSLPFAARLNTPMGPGRTVVVKGEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPGMYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSWSGPSSG 155
                                  |  -         -      | 11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
                                  7                   8

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 '\|'

NMR Structure

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)

d2yroa_

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

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Gal-bind_lectin (60)

Homo sapiens (Human) (25)

Gal-bind_lectin-2yroA01

A:18-148

NMR Structure(hide GO term definitions)

Chain A (LEG8_HUMAN | O00214)

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: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:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2yro)

	Sites
(no "Sites" information available for 2yro)

	Cis Peptide Bonds
		Leu A:17 - Pro A:18	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2yro
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LEG8_HUMAN \| O00214
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LEG8_HUMAN \| O00214
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 2YRO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (6, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

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