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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GALECTIN-3 CARBOHYDRATE-RECOGNITION DOMAIN AT 1.35 ANGSTROM RESOLUTION
 
Authors :  H. Blanchard, P. M. Collins
Date :  23 Oct 06  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Sandwich, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. M. Collins, K. I. P. J. Hidari, H. Blanchard
Slow Diffusion Of Lactose Out Of Galectin-3 Crystals Monitored By X-Ray Crystallography: Possible Implications For Ligand-Exchange Protocols
Acta Crystallogr. , Sect. D V. 63 415 2007
PubMed-ID: 17327679  |  Reference-DOI: 10.1107/S090744490605270X

(-) Compounds

Molecule 1 - GALECTIN-3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-3A
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGALECTIN-3 CRD DOMAIN, RESIDUES 113-250
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGALACTOSE-SPECIFIC LECTIN 3, MAC-2 ANTIGEN, IGE-BINDING PROTEIN, 35 KDA LECTIN, CARBOHYDRATE-BINDING PROTEIN 35, CBP 35, LAMININ-BINDING PROTEIN, LECTIN L-29, L-31, GALACTOSIDE-BINDING PROTEIN, GALBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CL1Ligand/IonCHLORIDE ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:158 , ASN A:160 , ARG A:162 , ASN A:174 , GLU A:184 , GOL A:400 , BGC A:501 , HOH A:554 , HOH A:637BINDING SITE FOR RESIDUE GAL A 500
2AC2SOFTWAREARG A:162 , GLU A:184 , GOL A:400 , GAL A:500 , HOH A:652BINDING SITE FOR RESIDUE BGC A 501
3AC3SOFTWARELYS A:226 , LYS A:227 , GOL A:300 , HOH A:537BINDING SITE FOR RESIDUE CL A 502
4AC4SOFTWAREARG A:151 , LYS A:227 , THR A:248 , MET A:249 , CL A:502 , HOH A:527 , HOH A:653BINDING SITE FOR RESIDUE GOL A 300
5AC5SOFTWAREHIS A:158 , ASN A:160 , ARG A:162 , ASN A:174 , GLU A:184 , GAL A:500 , BGC A:501 , HOH A:554BINDING SITE FOR RESIDUE GOL A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:116 -Pro A:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049768R183KLEG3_HUMANPolymorphism10148371AR183K

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG3_HUMAN118-248  1A:118-248

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002543011ENSE00001536507chr14:55595872-55596018147LEG3_HUMAN-00--
1.2bENST000002543012bENSE00001536493chr14:55604088-5560410922LEG3_HUMAN1-660--
1.2cENST000002543012cENSE00001002799chr14:55604763-55605086324LEG3_HUMAN7-1141081A:113-1142
1.3ENST000002543013ENSE00001757559chr14:55606993-5560708189LEG3_HUMAN115-144301A:115-14430
1.4ENST000002543014ENSE00001682369chr14:55609302-55609467166LEG3_HUMAN144-199561A:144-19956
1.5bENST000002543015bENSE00001786819chr14:55611834-55612147314LEG3_HUMAN200-250511A:200-25051

(-) 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:138
 aligned with LEG3_HUMAN | P17931 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:138
                                   122       132       142       152       162       172       182       192       202       212       222       232       242        
           LEG3_HUMAN   113 PLIVPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
               SCOP domains d2nmoa_ A: Galectin-3 CRD                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----Gal-bind_lectin-2nmoA01 A:117-247                                                                                                  --- Pfam domains
         Sec.struct. author .....eeee........eeeeeeeee......eeeeeee..eeeeeeeeeeee..eeeeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------K------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----GALECTIN  PDB: A:118-248 UniProt: 118-248                                                                                          -- PROSITE
           Transcript 1 (1) 1.Exon 1.3  PDB: A:115-144      -------------------------------------------------------Exon 1.5b  PDB: A:200-250 UniProt: 200-250          Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.4  PDB: A:144-199 UniProt: 144-199               --------------------------------------------------- Transcript 1 (2)
                 2nmo A 113 PLIVPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI 250
                                   122       132       142       152       162       172       182       192       202       212       222       232       242        

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LEG3_HUMAN | P17931)
molecular function
    GO:0019863    IgE binding    Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype.
    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:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    GO:0043236    laminin binding    Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells.
    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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0048245    eosinophil chemotaxis    The movement of an eosinophil in response to an external stimulus.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0048246    macrophage chemotaxis    The movement of a macrophage in response to an external stimulus.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0071674    mononuclear cell migration    The movement of a mononuclear cell within or between different tissues and organs of the body.
    GO:2001189    negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell    Any process that stops, prevents or reduces the frequency, rate or extent of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0045806    negative regulation of endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:2000521    negative regulation of immunological synapse formation    Any process that stops, prevents or reduces the frequency, rate or extent of immunological synapse formation.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0090280    positive regulation of calcium ion import    Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
    GO:2001200    positive regulation of dendritic cell differentiation    Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
    GO:0071677    positive regulation of mononuclear cell migration    Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body.
    GO:0070232    regulation of T cell apoptotic process    Any process that modulates the occurrence or rate of T cell death by apoptotic process.
    GO:0042129    regulation of T cell proliferation    Any process that modulates the frequency, rate or extent of T cell proliferation.
    GO:1902041    regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that modulates the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LEG3_HUMAN | P179311a3k 1kjl 1kjr 2nmn 2nn8 2xg3 3aya 3ayc 3ayd 3aye 3t1l 3t1m 3zsj 3zsk 3zsl 3zsm 4bli 4blj 4bm8 4jc1 4jck 4lbj 4lbk 4lbl 4lbm 4lbn 4lbo 4r9a 4r9b 4r9c 4r9d 4rl7 4xbn 5e88 5e89 5e8a 5exo 5h9p 5h9r 5iuq 5nf7 5nf9 5nfa 5nfb 5nfc

(-) Related Entries Specified in the PDB File

2nmn THE SAME PROTEIN BUT WITH WATER AND LACTOSE IN THE BINDING SITE (PARTIAL OCCUPANCY)
2nn8 THE SAME PROTEIN BUT WITH LACTOSE ONLY IN THE BINDING SITE