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(-) Description

Title :  CRYSTAL STRUCTURE OF TWO N-TERMINAL DOMAINS OF SIGLEC-5 IN COMPLEX WITH 6'-SIALYLLACTOSE
 
Authors :  M. A. Zhuravleva, P. D. Sun
Date :  17 Jan 08  (Deposition) - 05 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Siglec-5 Inhibitory Receptor, Two-Domain Structure, V-Set, C2-Set, Ig-Like Domain, Sialic Acid, 6'-Sialyllactose Complex, Cell Adhesion, Glycoprotein, Immunoglobulin Domain, Lectin, Membrane, Polymorphism, Transmembrane, Immune System/Carbohydrate Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Zhuravleva, K. Trandem, P. D. Sun
Structural Implications Of Siglec-5-Mediated Sialoglycan Recognition
J. Mol. Biol. V. 375 437 2008
PubMed-ID: 18022638  |  Reference-DOI: 10.1016/J.JMB.2007.10.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIALIC ACID-BINDING IG-LIKE LECTIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL V-SET AND C2-SET DOMAIN, UNP RESIDUES 20-233
    GeneSIGLEC5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSIGLEC-5, OBESITY-BINDING PROTEIN 2, OB-BINDING PROTEIN 2, OB-BP2, CD33 ANTIGEN-LIKE 2, CD170 ANTIGEN

 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
1SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:124 , LYS A:132 , TYR A:133 , SER A:134 , GLN A:136 , PRO A:209 , GLU A:210 , HOH A:254BINDING SITE FOR RESIDUE SIA A 241

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:41 -A:175
2A:46 -A:106
3A:169 -A:218

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZG1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014249V72ASIGL5_HUMANPolymorphism1973019AV77A
2UniProtVAR_014250M215VSIGL5_HUMANPolymorphism1807124AM220V

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZG1)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZG1)

(-) 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:208
 aligned with SIGL5_HUMAN | O15389 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:214
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
          SIGL5_HUMAN    20 VYELQVQKSVTVQEGLCVLVPCSFSYPWRSWYSSPPLYVYWFRDGEIPYYAEVVATNNPDRRVKPETQGRFRLLGDVQKKNCSLSIGDARMEDTGSYFFRVERGRDVKYSYQQNKLNLEVTALIEKPDIHFLEPLESGRPTRLSCSLPGSCEAGPPLTFSWTGNALSPLDPETTRSSELTLTPRPEDHGTNLTCQMKRQGAQVTTERTVQLNVS 233
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -V-set-2zg1A01 A:26-144                                                                                                 -----------------ig-2zg1A02 A:162-220                                       ------------------ Pfam domains
         Sec.struct. author ..eee...eeeee....eee..eee...........eeeeeee...hhhhh...ee..............eee..hhhhh...eee...hhhhheeeeeeeee...eeee.....eeeeee......eee--........eeeeee...........eeeee...............eeee.........eeeeeee..----..eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------V------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zg1 A  25 VYELQVQKSVTVQEGLCVLVPCSFSYPWRSWYSSPPLYVYWFRDGEIPYYAEVVATNNPDRRVKPETQGRFRLLGDVQKKNCSLSIGDARMEDTGSYFFRVERGRDVKYSYQQNKLNLEVTALIEKPDIH--EPLESGRPTRLSCSLPGSCEAGPPLTFSWTGNALSPLDPETTRSSELTLTPRPEDHGTNLTCQMKRQ----TTERTVQLNVS 238
                                    34        44        54        64        74        84        94       104       114       124       134       144       154  |    164       174       184       194       204       214        |-   |   234    
                                                                                                                                                           154  |                                                               223  228          
                                                                                                                                                              157                                                                                 

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ZG1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZG1)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SIGL5_HUMAN | O15389)
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:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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
        SIGL5_HUMAN | O153892zg2 2zg3

(-) Related Entries Specified in the PDB File

1o7s SIGLEC-7
1qfo SIGLEC-1
2zg2 N-TERMINAL V-SET AND C2-SET DOMAIN STRUCTURE OF NATIVE SIGLEC-5
2zg3 N-TERMINAL V-SET AND C2-SET DOMAIN STRUCTURE OF SIGLEC-5 IN COMPLEX WITH 3'-SIALYLLACTOSE