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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN GALECTIN-8
 
Authors :  S. Kishishita, A. Nishino, K. Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Apr 07  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Two Beta Sheets, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kishishita, A. Nishino, M. Kazutaka, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of N-Terminal Domain Of Human Galectin-8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GALECTIN-8 VARIANT
    ChainsA
    EngineeredYES
    Expression System PlasmidPK050620-06
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-165
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YV8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YV8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:24 -Pro A:25
2Lys A:64 -Pro A:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012990F19YLEG8_HUMANPolymorphism2737713AY26Y
2UniProtVAR_009710R36CLEG8_HUMANPolymorphism1041935AC43C
3UniProtVAR_012991M56VLEG8_HUMANPolymorphism1041937AV63V

  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.LEG8_HUMAN19-152
187-317
  1A:27-159
-

(-) Exons   (0, 0)

(no "Exon" information available for 2YV8)

(-) 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:151
 aligned with LEG8_HUMAN | O00214 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   
           LEG8_HUMAN     7 NLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSMKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSDLQSTQASSLELTEISRENVPKSG 179
               SCOP domains d2yv8a_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Gal-bind_lectin-2yv8A01 A:25-158                                                                                                      ---------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeee........eeeeeeee.......eeeeeee........eeeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee.----------------------.... Sec.struct. author
                 SAPs(SNPs) ------------Y----------------C-------------------V--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GALECTIN  PDB: A:27-159 UniProt: 19-152                                                                                               --------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv8 A  14 NLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVImVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSG----------------------PSSG 164
                                    23        33        43        53        63        73        83        93       103       113 |     123       133       143       153      |  -         -       161   
                                                                                                                               115-MSE                                      160                    161   

Chain A from PDB  Type:PROTEIN  Length:151
 aligned with Q59E97_HUMAN | Q59E97 from UniProtKB/TrEMBL  Length:338

    Alignment length:173
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197   
         Q59E97_HUMAN    28 NLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFSSDLQSTQASSLELTEISRENVPKSG 200
               SCOP domains d2yv8a_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Gal-bind_lectin-2yv8A01 A:25-158                                                                                                      ---------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeee........eeeeeeee.......eeeeeee........eeeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee.----------------------.... Sec.struct. author
                 SAPs(SNPs) ------------Y----------------C-------------------V--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv8 A  14 NLQNIIYNPVIPYVGTIPDQLDPGTLIVICGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVImVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSG----------------------PSSG 164
                                    23        33        43        53        63        73        83        93       103       113 |     123       133       143       153      |  -         -       161   
                                                                                                                               115-MSE                                      160                    161   

   Legend:   → Mismatch (orange background)
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    → 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 2YV8)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q59E97_HUMAN | Q59E97)
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.

Chain A   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        LEG8_HUMAN | O002142yro 2yxs 3ap4 3ap5 3ap6 3ap7 3ap9 3apb 3ojb 3vkl 3vkm 3vkn 3vko 4bmb 4bme 4fqz 4gxl 4han 5gzc 5gzd 5gze 5gzf 5gzg 5t7i 5t7s 5t7t 5t7u
        Q59E97_HUMAN | Q59E972yxs

(-) Related Entries Specified in the PDB File

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