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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF R111H HUMAN GALECTIN-1
 
Authors :  M. I. F. Lopez-Lucendo, H. J. Gabius, A. Romero
Date :  21 Aug 04  (Deposition) - 20 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lectin, Carbohydrate-Binding Proteins, Galactosides, Galectin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. I. F. Lopez-Lucendo, D. Solis, S. Andre, J. Hirabayashi, K. Kasai, H. Kaltner, H. J. Gabius, A. Romero
Growth-Regulatory Human Galectin-1: Crystallographic Characterisation Of The Structural Changes Induced By Single-Site Mutations And Their Impact On The Thermodynamics Of Ligand Binding
J. Mol. Biol. V. 343 957 2004
PubMed-ID: 15476813  |  Reference-DOI: 10.1016/J.JMB.2004.08.078

(-) Compounds

Molecule 1 - GALECTIN-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPH14GAL
    Expression System StrainSCS1
    Expression System Taxid562
    Expression System VectorPUC540
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-GALACTOSIDE-BINDING LECTIN L-14-I, HPL, LACTOSE-BINDING LECTIN 1, S-LAC LECTIN 1, GALAPTIN, HBL
 
Molecule 2 - GALECTIN-1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPH14GAL
    Expression System StrainSCS1
    Expression System Taxid562
    Expression System VectorPUC540
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-GALACTOSIDE-BINDING LECTIN L-14-I, HPL, LACTOSE-BINDING LECTIN 1, S-LAC LECTIN 1, GALAPTIN, HBL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1060 , GLN A:1072 , GLU A:1074BINDING SITE FOR RESIDUE BME A2135
2AC2SOFTWAREVAL A:1087 , CYS A:1088 , LYS A:1099 , LEU A:1100 , PRO A:1101 , HOH A:2054BINDING SITE FOR RESIDUE BME A2136
3AC3SOFTWAREARG A:1018 , VAL A:1019 , ARG A:1020 , CYS A:1130 , VAL A:1131 , ALA A:1132 , PRO B:2025BINDING SITE FOR RESIDUE BME A2137
4AC4SOFTWARECYS B:2016 , CYS B:2088 , ILE B:2089BINDING SITE FOR RESIDUE BME B3135
5AC5SOFTWAREGLU B:2086 , CYS B:2088 , PRO B:2101 , HOH B:4068BINDING SITE FOR RESIDUE BME B3136
6AC6SOFTWAREARG B:2018 , ARG B:2020 , ASP B:2026 , GLU B:2086 , CYS B:2130 , ALA B:2132BINDING SITE FOR RESIDUE BME B3137

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W6Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG1_HUMAN4-135
 
  2A:1003-1134
B:2003-2134

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002159091aENSE00001045616chr22:38071615-38071718104LEG1_HUMAN1-332A:1001-1002
B:2001-2002
2
2
1.3bENST000002159093bENSE00001258442chr22:38072993-3807307280LEG1_HUMAN4-30272A:1003-1029
B:2003-2029
27
27
1.5cENST000002159095cENSE00001746974chr22:38074490-38074661172LEG1_HUMAN30-87582A:1029-1086
B:2029-2086
58
58
1.6cENST000002159096cENSE00001173615chr22:38075610-38075813204LEG1_HUMAN88-135482A:1087-1134
B:2087-2134
48
48

(-) 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:134
 aligned with LEG1_HUMAN | P09382 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
          LEG1_HUMAN      2 ACGLVASNLNLKPGECLRVRGEVAPDAKSFVLNLGKDSNNLCLHFNPRFNAHGDANTIVCNSKDGGAWGTEQREAVFPFQPGSVAEVCITFDQANLTVKLPDGYEFKFPNRLNLEAINYMAADGDFKIKCVAFD  135
               SCOP domains d1w6qa_ A: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1w6qA00 A:1001-1134  [code=2.60.120.200, no name defined]                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeee..ee...eee........eeeeeeeee...eeeee.....eeeee.......eeeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: A:1003-1134 UniProt: 4-135                                                                                            PROSITE
           Transcript 1 (1) 1.Exon 1.3b  PDB: A:1003-1029---------------------------------------------------------Exon 1.6c  PDB: A:1087-1134 UniProt: 88-135      Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.5c  PDB: A:1029-1086 UniProt: 30-87                ------------------------------------------------ Transcript 1 (2)
                1w6q A 1001 ACGLVASNLNLKPGEcLRVRGEVAPDAKSFVLNLGKDSNNLCLHFNPRFNAHGDANTIVCNSKDGGAWGTEQREAVFPFQPGSVAEVCITFDQANLTVKLPDGYEFKFPNHLNLEAINYMAADGDFKIKCVAFD 1134
                                  1010     |1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130    
                                        1016-CSO                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with LEG1_HUMAN | P09382 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
          LEG1_HUMAN      2 ACGLVASNLNLKPGECLRVRGEVAPDAKSFVLNLGKDSNNLCLHFNPRFNAHGDANTIVCNSKDGGAWGTEQREAVFPFQPGSVAEVCITFDQANLTVKLPDGYEFKFPNRLNLEAINYMAADGDFKIKCVAFD  135
               SCOP domains d1w6qb_ B: Galectin-1                                                                                                                  SCOP domains
               CATH domains 1w6qB00 B:2001-2134  [code=2.60.120.200, no name defined]                                                                              CATH domains
           Pfam domains (1) --Gal-bind_lectin-1w6qB01 B:2003-2133                                                                                                - Pfam domains (1)
           Pfam domains (2) --Gal-bind_lectin-1w6qB02 B:2003-2133                                                                                                - Pfam domains (2)
         Sec.struct. author ....eeeeeee.....eeeeeee......eeeeeeee..eeeeeeeeeee....eeeeeeeeee...................eeeeeeee...eeeee.....eeeee.......eeeeeeee.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: B:2003-2134 UniProt: 4-135                                                                                            PROSITE
           Transcript 1 (1) 1.Exon 1.3b  PDB: B:2003-2029---------------------------------------------------------Exon 1.6c  PDB: B:2087-2134 UniProt: 88-135      Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.5c  PDB: B:2029-2086 UniProt: 30-87                ------------------------------------------------ Transcript 1 (2)
                1w6q B 2001 ACGLVASNLNLKPGECLRVRGEVAPDAKSFVLNLGKDSNNLCLHFNPRFNAHGDANTIVCNSKDGGAWGTEQREAVFPFQPGSVAEVCITFDQANLTVKLPDGYEFKFPNHLNLEAINYMAADGDFKIKCVAFD 2134
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130    

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEG1_HUMAN | P09382)
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:0030395    lactose binding    Interacting selectively and non-covalently with lactose, a disaccharide of glucose and galactose, the carbohydrate of milk.
    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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0071333    cellular response to glucose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0033555    multicellular organismal response to stress    Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    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:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    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:2001200    positive regulation of dendritic cell differentiation    Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation.
    GO:0034120    positive regulation of erythrocyte aggregation    Any process that activates or increases the frequency, rate, or extent of erythrocyte aggregation.
    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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0048678    response to axon injury    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an axon injury stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        LEG1_HUMAN | P093821gzw 1w6m 1w6n 1w6o 1w6p 2km2 2zkn 3oy8 3oyw 3t2t 3w58 3w59 4q1p 4q1r 4q26 4q27 4q2f 4xbl 4y1u 4y1v 4y1x 4y1y 4y1z 4y20 4y22 4y24

(-) Related Entries Specified in the PDB File

1gzw X-RAY CRYSTAL STRUCTURE OF HUMAN GALECTIN-1
1w6m X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH GALACTOSE
1w6n X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1
1w6o X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH LACTOSE
1w6p X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH N-ACETYL- LACTOSAMINE