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Asym./Biol. Unit

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Asym./Biol. Unit - sites (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF THE GALECTIN-8 N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH LACTOSE SIALIC ACID

Authors :   T. Matsuzaka, H. Ideo, K. Yamashita, T. Nonaka

Date :   12 Oct 10 (Deposition) - 26 Jan 11 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym./Biol. Unit : A

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

Reference :   H. Ideo, T. Matsuzaka, T. Nonaka, A. Seko, K. Yamashita
Galectin-8-N-Domain Recognition Mechanism For Sialylated An Sulfated Glycans
J. Biol. Chem. V. 286 11346 2011
PubMed-ID: 21288902 | Reference-DOI: 10.1074/JBC.M110.195925

Compounds

Molecule 1 - GALECTIN-8
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN
	Gene	:	LGALS8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAL-8, PO66 CARBOHYDRATE-BINDING PROTEIN, PO66-CBP, PROSTATE CARCINOMA TUMOR ANTIGEN 1, PCTA-1

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	LAT	1	Ligand/Ion	BETA-LACTOSE
3	SIA	1	Ligand/Ion	O-SIALIC ACID

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:45 , HIS A:65 , ASN A:67 , ARG A:69 , ASN A:79 , GLU A:89 , SIA A:156 , HOH A:295 , HOH A:313 , HOH A:353	BINDING SITE FOR RESIDUE LAT A 155
2	AC2	SOFTWARE	ARG A:45 , GLN A:47 , ARG A:59 , TRP A:86 , LAT A:155 , HOH A:357 , HOH A:378	BINDING SITE FOR RESIDUE SIA A 156
3	AC3	SOFTWARE	ASP A:112 , HOH A:319	BINDING SITE FOR RESIDUE CL A 157

SS Bonds (0, 0)

(no "SS Bond" information available for 3AP7)

Cis Peptide Bonds (2, 2)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:17	-	Pro A:18
2	Lys A:57	-	Pro A:58

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012990	F	19	Y	LEG8_HUMAN	Polymorphism	2737713	A	F	19	Y
2	UniProt	VAR_009710	R	36	C	LEG8_HUMAN	Polymorphism	1041935	A	R	36	C
3	UniProt	VAR_012991	M	56	V	LEG8_HUMAN	Polymorphism	1041937	A	V	56	V

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

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (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:19-152 -

Exons (4, 4)

Asymmetric/Biological Unit (4, 4)

	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	1	A:4-15	12
1.7b	ENST00000366584	7b	ENSE00002141991	chr1:236700797-236700885	89	LEG8_HUMAN	16-45	30	1	A:16-45	30
1.8b	ENST00000366584	8b	ENSE00000793501	chr1:236702179-236702389	211	LEG8_HUMAN	45-115	71	1	A:45-115	71
1.9b	ENST00000366584	9b	ENSE00000805377	chr1:236703864-236703983	120	LEG8_HUMAN	116-155	40	1	A:116-154	39
1.10e	ENST00000366584	10e	ENSE00000793503	chr1:236704954-236705010	57	LEG8_HUMAN	156-174	19	0	-	-
1.11c	ENST00000366584	11c	ENSE00001226656	chr1:236706061-236706087	27	LEG8_HUMAN	175-183	9	0	-	-
1.11r	ENST00000366584	11r	ENSE00002191373	chr1:236706860-236706948	89	LEG8_HUMAN	184-213	30	0	-	-
1.12c	ENST00000366584	12c	ENSE00000805385	chr1:236708050-236708215	166	LEG8_HUMAN	213-268	56	0	-	-
1.14j	ENST00000366584	14j	ENSE00001911385	chr1:236711312-236714310	2999	LEG8_HUMAN	269-317	49	0	-	-

Sequences/Alignments

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:151
 aligned with LEG8_HUMAN | O00214 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:151
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 
           LEG8_HUMAN     4 SLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFS 154
               SCOP domains d3ap7a_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeee.........eeeeeee.......eeeeee..........eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------Y----------------C-------------------V-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------GALECTIN  PDB: A:19-152 UniProt: 19-152                                                                                               -- PROSITE
           Transcript 1 (1) Exon 1.6a   Exon 1.7b  PDB: A:16-45       ----------------------------------------------------------------------Exon 1.9b  PDB: A:116-154 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.8b  PDB: A:45-115 UniProt: 45-115                               --------------------------------------- Transcript 1 (2)
                 3ap7 A   4 SLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFS 154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological 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)

d3ap7a_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3AP7)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3AP7)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(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.

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	Cis Peptide Bonds
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		Lys A:57 - Pro A:58	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	LEG8_HUMAN \| O00214	:	2yro 2yv8 2yxs 3ap4 3ap5 3ap6 3ap9 3apb 3ojb 3vkl 3vkm 3vkn 3vko 4bmb 4bme 4fqz 4gxl 4han 5gzc 5gzd 5gze 5gzf 5gzg 5t7i 5t7s 5t7t 5t7u

Related Entries Specified in the PDB File

3ap4	THE SAME PROTEIN COMPLEXED WITH LACTOSE.
3ap5	THE SAME PROTEIN IN APO FORM.
3ap6	THE SAME PROTEIN COMPLEXED WITH LACTOSE 3'-SULFATE.