1SLT - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF S-LECTIN, A DEVELOPMENTALLY REGULATED VERTEBRATE BETA-GALACTOSIDE BINDING PROTEIN

Authors :   D. -I. Liao, O. Herzberg

Date :   20 Oct 93 (Deposition) - 31 Jan 94 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. I. Liao, G. Kapadia, H. Ahmed, G. R. Vasta, O. Herzberg
Structure Of S-Lectin, A Developmentally Regulated Vertebrate Beta-Galactoside-Binding Protein.
Proc. Natl. Acad. Sci. Usa V. 91 1428 1994
PubMed-ID: 8108426 | Reference-DOI: 10.1073/PNAS.91.4.1428
(for further references see the PDB file header)

Molecule 1 - BOVINE GALECTIN-1
	Chains	:	A, B
	Engineered	:	YES
	Organism Common	:	COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	SPLEEN

		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 (4, 11)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	OCS	6	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	OCS	6	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	OCS	3	Mod. Amino Acid	CYSTEINESULFONIC ACID

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	OCS	3	Mod. Amino Acid	CYSTEINESULFONIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , ARG A:48 , GLU A:71 , ARG A:73 , ASN A:118 , GAL A:402 , HOH A:506 , HOH A:533 , HOH A:579	BINDING SITE FOR RESIDUE NDG A 401
2	AC2	SOFTWARE	HIS A:44 , ASN A:46 , ARG A:48 , ASN A:61 , TRP A:68 , GLU A:71 , NDG A:401 , HOH A:516	BINDING SITE FOR RESIDUE GAL A 402
3	AC3	SOFTWARE	VAL A:55 , LEU A:112 , HOH A:559 , ARG B:48 , GLU B:71 , ARG B:73 , GAL B:412 , HOH B:417 , HOH B:425 , HOH B:443 , HOH B:467	BINDING SITE FOR RESIDUE NDG B 411
4	AC4	SOFTWARE	ASP A:64 , HIS B:44 , ASN B:46 , ARG B:48 , ASN B:61 , TRP B:68 , GLU B:71 , NDG B:411 , HOH B:422 , HOH B:474	BINDING SITE FOR RESIDUE GAL B 412
5	AC5	SOFTWARE	LYS B:28	BINDING SITE FOR RESIDUE CL A 500
6	SB1	AUTHOR	HIS A:44 , ASN A:46 , ARG A:48 , HIS A:52 , ASP A:54 , VAL A:59 , CYS A:60 , ASN A:61 , TRP A:68 , GLU A:71 , ARG A:73	CARBOHYDRATE BINDING SITE IN MOLECULES A
7	SB2	AUTHOR	HIS B:44 , ASN B:46 , ARG B:48 , HIS B:52 , ASP B:54 , VAL B:59 , CYS B:60 , ASN B:61 , TRP B:68 , GLU B:71 , ARG B:73	CARBOHYDRATE BINDING SITE IN MOLECULES B

(no "SS Bond" information available for 1SLT)

(no "Cis Peptide Bond" information available for 1SLT)

(no "SAP(SNP)/Variant" information available for 1SLT)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEG1_BOVIN	4-135	2	A:3-134 B:3-134

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.	LEG1_BOVIN	4-135	2	A:3-134 B:3-134

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.	LEG1_BOVIN	4-135	1	A:3-134 -

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.	LEG1_BOVIN	4-135	1	- B:3-134

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000020080	1	ENSBTAE00000163579	chr5:116534343-116535003	661	LEG1_BOVIN	1-58	58	2	A:2-57 B:3-57	56 55
1.2	ENSBTAT00000020080	2	ENSBTAE00000163587	chr5:116535341-116535537	197	LEG1_BOVIN	59-106	48	2	A:58-105 B:58-105	48 48

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
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Chain A from PDB  Type:PROTEIN  Length:133
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:133
                                    12        22        32        42        52        62        72        82        92       102       112       122       132   
           LEG1_BOVIN     3 CGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1slta_ A: Galectin-1                                                                                                                 SCOP domains
               CATH domains 1sltA00 A:2-134  [code=2.60.120.200, no name defined]                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................................................................eeeeeeee...eeeee.....eeeee................eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: A:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-57 UniProt: 1-58 [INCOMPLETE]        Exon 1.2  PDB: A:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slt A   2 CGLVASNLNLKPGEcLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVcISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKcVAFE 134
                                    11    |   21        31        41        51        61        71        81      | 91       101       111       121       131   
                                         16-OCS                                                                  88-OCS                                   130-OCS

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:132
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  
           LEG1_BOVIN     4 GLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1sltb_ B: Galectin-1                                                                                                                SCOP domains
               CATH domains 1sltB00 B:3-134  [code=2.60.120.200, no name defined]                                                                                CATH domains
           Pfam domains (1) Gal-bind_lectin-1sltB01 B:3-133                                                                                                    - Pfam domains (1)
           Pfam domains (2) Gal-bind_lectin-1sltB02 B:3-133                                                                                                    - Pfam domains (2)
         Sec.struct. author .................................................................................eeeeeeee...eeeee.....eeeee................eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GALECTIN  PDB: B:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-57 UniProt: 1-58 [INCOMPLETE]       Exon 1.2  PDB: B:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slt B   3 GLVASNLNLKPGEcLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVcISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKcVAFE 134
                                    12   |    22        32        42        52        62        72        82     |  92       102       112       122       132  
                                        16-OCS                                                                  88-OCS                                   130-OCS

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-1 (22)

Cow (Bos taurus) [TaxId: 9913] (4)

1a	d1slta_	A:
1b	d1sltb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Cow (Bos taurus) (4)

1a	1sltA00	A:2-134
1b	1sltB00	B:3-134

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Gal-bind_lectin (60)

Bos taurus (Bovine) (3)

1a	Gal-bind_lectin-1sltB01	B:3-133
1b	Gal-bind_lectin-1sltB02	B:3-133

Asymmetric Unit(hide GO term definitions)

Chain A,B (LEG1_BOVIN | P11116)

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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0045445	myoblast differentiation	The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
	GO:0002317	plasma cell differentiation	The process in which a B cell acquires the specialized features of a plasma cell. A plasma cell is a lymphocyte which develops from a B cell and produces high amounts of antibody.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0046598	positive regulation of viral entry into host cell	Any process that activates or increases the frequency, rate or extent of the introduction of viral entry into the host cell.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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: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:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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