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Title :   CRYSTAL STRUCTURE OF THE N TERMINAL DOMAIN OF HUMAN GALECTIN 8, F19Y MUTANT

Authors :   E. Buzamet, F. M. Ruiz, M. Menendez, A. Romero, H. J. Gabius, D. Solis

Date :   07 May 13 (Deposition) - 19 Mar 14 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   F. M. Ruiz, B. A. Scholz, E. Buzamet, J. Kopitz, S. Andre, M. Menendez, A. Romero, D. Solis, H. J. Gabius
Natural Single Amino Acid Polymorphism (F19Y) In Human Galectin-8: Detection Of Structural Alterations And Increased Growth-Regulatory Activity On Tumor Cells.
Febs J. V. 281 1446 2014
PubMed-ID: 24418318 | Reference-DOI: 10.1111/FEBS.12716

Molecule 1 - GALECTIN-8
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N TERMINAL DOMAIN, RESIDUES 4-155
	Mutation	:	YES
	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

		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 (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (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	ARG A:45 , HIS A:65 , ASN A:67 , ARG A:69 , ASN A:79 , GLU A:89 , HOH A:2016	BINDING SITE FOR RESIDUE LBT A1156
2	AC2	SOFTWARE	ARG B:45 , HIS B:65 , ASN B:67 , ARG B:69 , ASN B:79 , GLU B:89 , HOH B:2013	BINDING SITE FOR RESIDUE LBT B1154

(no "SS Bond" information available for 4BME)

Asymmetric Unit

No.	Residues
1	Ile A:17	-	Pro A:18
2	Lys A:57	-	Pro A:58
3	Ile B:17	-	Pro B:18
4	Lys B:57	-	Pro B:58
5	Arg B:72	-	Ala B:73

Asymmetric Unit (3, 6)

								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/B	Y	19	Y
2	UniProt	VAR_009710	R	36	C	LEG8_HUMAN	Polymorphism	1041935	A/B	R	36	C
3	UniProt	VAR_012991	M	56	V	LEG8_HUMAN	Polymorphism	1041937	A/B	M	56	V

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

Biological Unit 1 (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	Y	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	M	56	V

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

Biological Unit 2 (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	B	Y	19	Y
2	UniProt	VAR_009710	R	36	C	LEG8_HUMAN	Polymorphism	1041935	B	R	36	C
3	UniProt	VAR_012991	M	56	V	LEG8_HUMAN	Polymorphism	1041937	B	M	56	V

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.	LEG8_HUMAN	19-152 187-317	2	A:20-152 B:20-152 -

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.	LEG8_HUMAN	19-152 187-317	1	A:20-152 - -

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.	LEG8_HUMAN	19-152 187-317	1	- B:20-152 -

Asymmetric Unit (4, 8)

	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	2	A:7-15 B:7-15	9 9
1.7b	ENST00000366584	7b	ENSE00002141991	chr1:236700797-236700885	89	LEG8_HUMAN	16-45	30	2	A:16-45 B:16-45	30 30
1.8b	ENST00000366584	8b	ENSE00000793501	chr1:236702179-236702389	211	LEG8_HUMAN	45-115	71	2	A:45-115 (gaps) B:45-115 (gaps)	71 71
1.9b	ENST00000366584	9b	ENSE00000805377	chr1:236703864-236703983	120	LEG8_HUMAN	116-155	40	2	A:116-155 B:116-153	40 38
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	-	-

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:147
 aligned with LEG8_HUMAN | O00214 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:149
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146         
           LEG8_HUMAN     7 NLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSS 155
               SCOP domains d4bmea_ 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:20-152 UniProt: 19-152                                                                                               --- PROSITE
           Transcript 1 (1) Exon 1.6aExon 1.7b  PDB: A:16-45       ----------------------------------------------------------------------Exon 1.9b  PDB: A:116-155                Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8b  PDB: A:45-115 (gaps) UniProt: 45-115                        ---------------------------------------- Transcript 1 (2)
                 4bme A   7 NLQNIIYNPVIPYVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFK--GCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSS 155
                                    16        26        36        46        56        66    |  |76        86        96       106       116       126       136       146         
                                                                                           71 74

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with LEG8_HUMAN | O00214 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:147
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       
           LEG8_HUMAN     7 NLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSF 153
               SCOP domains d4bmeb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeee.........eeeeeee.......eeeeeee........eeeeeeeee.....eeeeeeee..ee...eee.-.......eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------Y----------------C-------------------V------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GALECTIN  PDB: B:20-152 UniProt: 19-152                                                                                               - PROSITE
           Transcript 1 (1) Exon 1.6aExon 1.7b  PDB: B:16-45       ----------------------------------------------------------------------Exon 1.9b  PDB: B:116-153 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.8b  PDB: B:45-115 (gaps) UniProt: 45-115                        -------------------------------------- Transcript 1 (2)
                 4bme B   7 NLQNIIYNPVIPYVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITY-TPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSF 153
                                    16        26        36        46        56        66        76        86      | 96       106       116       126       136       146       
                                                                                                                 93 |                                                          
                                                                                                                   95

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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)

1a	d4bmea_	A:
1b	d4bmeb_	B:

(no "CATH Domain" information available for 4BME)

(no "Pfam Domain" information available for 4BME)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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4bmb	CRYSTAL STRUCTURE OF THE N TERMINAL DOMAIN OF HUMAN GALECTIN 8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (1, 2)

Exons (4, 8)

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Gene Ontology (8, 8)

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