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(-) Description

Title :  X-RAY CRYSTALLOGRAPHY REVEALS CROSSLINKING OF MAMMALIAN LECTIN (GALECTIN-1) BY BIANTENNARY COMPLEX TYPE SACCHARIDES
 
Authors :  Y. Bourne, C. Cambillau
Date :  12 Mar 94  (Deposition) - 26 Jan 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Complex(Lectin-Saccharide), Complex(Lectin-Saccharide) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Bourne, B. Bolgiano, D. I. Liao, G. Strecker, P. Cantau, O. Herzberg T. Feizi, C. Cambillau
Crosslinking Of Mammalian Lectin (Galectin-1) By Complex Biantennary Saccharides.
Nat. Struct. Biol. V. 1 863 1994
PubMed-ID: 7773775  |  Reference-DOI: 10.1038/NSB1294-863
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL4Ligand/IonBETA-D-GALACTOSE
3MAN5Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:48 , GLU A:71 , ARG A:73 , GAL A:352 , MAN A:353 , NAG A:355 , GLY B:66BINDING SITE FOR RESIDUE NAG A 351
02AC2SOFTWAREHIS A:44 , ASN A:46 , ARG A:48 , HIS A:52 , ASN A:61 , GLU A:71 , NAG A:351 , HOH A:780 , HOH A:818 , HOH A:841 , ASN B:39BINDING SITE FOR RESIDUE GAL A 352
03AC3SOFTWARENAG A:351 , BMA A:354 , NAG A:355 , HOH A:877 , HOH B:149 , NAG C:361BINDING SITE FOR RESIDUE MAN A 353
04AC4SOFTWAREMAN A:353 , NAG A:355 , MAN A:763 , HOH A:877 , HIS D:52 , GLY D:53 , HOH D:197BINDING SITE FOR RESIDUE BMA A 354
05AC5SOFTWAREGLY A:53 , ARG A:73 , NAG A:351 , MAN A:353 , BMA A:354 , HOH A:877 , HOH A:882BINDING SITE FOR RESIDUE NAG A 355
06AC6SOFTWAREBMA A:354 , NAG A:761 , HOH B:164BINDING SITE FOR RESIDUE MAN A 763
07AC7SOFTWAREGAL A:762 , MAN A:763 , HOH A:860 , GLY B:69 , ARG D:48 , GLU D:71 , ARG D:73 , HOH D:200BINDING SITE FOR RESIDUE NAG A 761
08AC8SOFTWARENAG A:761 , HOH B:150 , HOH B:165 , HIS D:44 , ASN D:46 , ARG D:48 , HIS D:52 , ASN D:61 , GLU D:71 , HOH D:144 , HOH D:199BINDING SITE FOR RESIDUE GAL A 762
09AC9SOFTWAREMAN A:353 , ARG B:48 , GLU B:71 , ARG B:73 , GAL C:362 , MAN C:363BINDING SITE FOR RESIDUE NAG C 361
10BC1SOFTWAREHIS B:44 , ASN B:46 , ARG B:48 , HIS B:52 , VAL B:59 , ASN B:61 , TRP B:68 , GLU B:71 , HOH B:145 , HOH B:160 , NAG C:361BINDING SITE FOR RESIDUE GAL C 362
11BC2SOFTWARENAG C:361 , MAN C:364 , HOH D:161 , HOH D:163BINDING SITE FOR RESIDUE MAN C 363
12BC3SOFTWAREMAN C:363 , MAN C:753 , HOH C:842BINDING SITE FOR RESIDUE MAN C 364
13BC4SOFTWAREMAN C:364 , NAG C:751 , HOH C:809 , HOH D:170 , HOH D:175BINDING SITE FOR RESIDUE MAN C 753
14BC5SOFTWAREARG C:48 , GLU C:71 , ARG C:73 , GAL C:752 , MAN C:753BINDING SITE FOR RESIDUE NAG C 751
15BC6SOFTWAREHIS C:44 , ASN C:46 , ARG C:48 , HIS C:52 , ASN C:61 , GLU C:71 , NAG C:751 , HOH C:765 , HOH C:767BINDING SITE FOR RESIDUE GAL C 752
16G1CUNKNOWNARG A:48 , GLU A:71 , ARG A:73 , ARG C:48 , GLU C:71 , ARG C:73NULL
17GA1UNKNOWNHIS A:44 , ASN A:46 , ARG A:48 , TRP A:68 , ASN A:61 , GLU A:71 , HIS C:44 , ASN C:46 , ARG C:48 , TRP C:68 , ASN C:61 , GLU C:71NULL
18GA2UNKNOWNHIS B:44 , ASN B:46 , ARG B:48 , TRP B:68 , ASN B:61 , GLU B:71 , HIS D:44 , ASN D:46 , ARG D:48 , TRP D:68 , ASN D:61 , GLU D:71NULL
19GC2UNKNOWNARG B:48 , GLU B:71 , ARG B:73 , ARG D:48 , GLU D:71 , ARG D:73NULL
20MN1UNKNOWNGLY A:53 , GLY C:53NULL
21MN2UNKNOWNGLY B:53 , GLY D:53NULL

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:16 -B:88

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG1_BOVIN4-135
 
 
 		  4A:3-134
B:3-134
C:3-134
D:3-134
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG1_BOVIN4-135
 
 
 		  2A:3-134
B:3-134
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG1_BOVIN4-135
 
 
 		  2-
-
C:3-134
D:3-134

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000200801ENSBTAE00000163579chr5:116534343-116535003661LEG1_BOVIN1-58584A:1-57
B:1-57
C:1-57
D:1-57		57
57
57
57
1.2ENSBTAT000000200802ENSBTAE00000163587chr5:116535341-116535537197LEG1_BOVIN59-106484A:58-105
B:58-105
C:58-105
D:58-105		48
48
48
48

(-) Sequences/Alignments

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:134
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LEG1_BOVIN     2 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1slba_ A: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1slbA00 A:1-134  [code=2.60.120.200, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeee..eeeeeeee........eeeeeeeee...eeeee.hhh.eeeee.......eeeeeeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: A:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-57 UniProt: 1-58 [INCOMPLETE]         Exon 1.2  PDB: A:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slb A   1 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LEG1_BOVIN     2 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1slbb_ B: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1slbB00 B:1-134  [code=2.60.120.200, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeee..eeeeeeee........eeeeeeeee...eeeee.....eeeee.......eeeeeeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: B:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-57 UniProt: 1-58 [INCOMPLETE]         Exon 1.2  PDB: B:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slb B   1 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain C from PDB  Type:PROTEIN  Length:134
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LEG1_BOVIN     2 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1slbc_ C: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1slbC00 C:1-134  [code=2.60.120.200, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeee..eeeeeeee........eeeeeeeee...eeeee.....eeeee.......eeeeeeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: C:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-57 UniProt: 1-58 [INCOMPLETE]         Exon 1.2  PDB: C:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slb C   1 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with LEG1_BOVIN | P11116 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LEG1_BOVIN     2 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 135
               SCOP domains d1slbd_ D: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1slbD00 D:1-134  [code=2.60.120.200, no name defined]                                                                                  CATH domains
           Pfam domains (1) --Gal-bind_lectin-1slbD01 D:3-133                                                                                                    - Pfam domains (1)
           Pfam domains (2) --Gal-bind_lectin-1slbD02 D:3-133                                                                                                    - Pfam domains (2)
           Pfam domains (3) --Gal-bind_lectin-1slbD03 D:3-133                                                                                                    - Pfam domains (3)
           Pfam domains (4) --Gal-bind_lectin-1slbD04 D:3-133                                                                                                    - Pfam domains (4)
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeee..eeeeeeee........eeeeeeeee...eeeee.....eeeee.......eeeeeeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: D:3-134 UniProt: 4-135                                                                                                PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-57 UniProt: 1-58 [INCOMPLETE]         Exon 1.2  PDB: D:58-105 UniProt: 59-106         ----------------------------- Transcript 1
                 1slb D   1 ACGLVASNLNLKPGECLRVRGEVAADAKSFLLNLGKDDNNLCLHFNPRFNAHGDVNTIVCNSKDAGAWGAEQRESAFPFQPGSVVEVCISFNQTDLTIKLPDGYEFKFPNRLNLEAINYLSAGGDFKIKCVAFE 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  LEG1_BOVIN | P11116
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        LEG1_BOVIN | P11116: 1sla 1slc 1slt

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