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(-) Description

Title :  SAMBUCUS NIGRA AGGLUTININ II (SNA-II), TETRAGONAL CRYSTAL FORM
 
Authors :  L. Maveyraud, V. Guillet, L. Mourey
Date :  19 Feb 08  (Deposition) - 25 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Trefoil, Ricin-B Domain, Glycosylation, Glycoprotein, Lectin, Sugar Binding Protein, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Maveyraud, H. Niwa, V. Guillet, D. I. Svergun, P. V. Konarev, R. A. Palmer, W. J. Peumans, P. Rouge, E. J. Van Damme, C. D. Reynolds, L. Mourey
Structural Basis For Sugar Recognition, Including The Tn Carcinoma Antigen, By The Lectin Sna-Ii From Sambucus Nigra
Proteins V. 75 89 2009
PubMed-ID: 18798567  |  Reference-DOI: 10.1002/PROT.22222

(-) Compounds

Molecule 1 - AGGLUTININ II
    Chains: A
    Organism Common: EUROPEAN ELDER, ELDERBERRY
    Organism Scientific: SAMBUCUS NIGRA
    Synonym: SNA-II
    Tissue: BARK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO44Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:21 , ASN A:63 , ASP A:114 , NAG A:259 , FUC A:260BINDING SITE FOR RESIDUE NAG A 258
02AC2SOFTWARENAG A:258 , FUC A:260 , HOH A:1051 , HOH A:1097BINDING SITE FOR RESIDUE NAG A 259
03AC3SOFTWARENAG A:258 , NAG A:259BINDING SITE FOR RESIDUE FUC A 260
04AC4SOFTWAREASN A:71 , SER A:73 , NAG A:262 , FUC A:263 , SO4 A:901BINDING SITE FOR RESIDUE NAG A 261
05AC5SOFTWARENAG A:261 , FUC A:263BINDING SITE FOR RESIDUE NAG A 262
06AC6SOFTWARENAG A:261 , NAG A:262 , SO4 A:901BINDING SITE FOR RESIDUE FUC A 263
07AC7SOFTWAREVAL A:133 , GLN A:166 , ASN A:178 , ARG A:181 , PRO A:257 , NAG A:265 , HOH A:957BINDING SITE FOR RESIDUE NAG A 264
08AC8SOFTWARENAG A:264BINDING SITE FOR RESIDUE NAG A 265
09AC9SOFTWAREASN A:232 , SER A:234 , LEU A:235BINDING SITE FOR RESIDUE NAG A 266
10BC1SOFTWAREASN A:71 , CYS A:72 , SER A:73 , NAG A:261 , FUC A:263 , HOH A:946BINDING SITE FOR RESIDUE SO4 A 901
11BC2SOFTWAREARG A:18 , ASN A:19 , ARG A:103 , ARG A:107 , THR A:108 , ILE A:109 , HOH A:965 , HOH A:1015 , HOH A:1016BINDING SITE FOR RESIDUE SO4 A 902
12BC3SOFTWARESER A:162 , LEU A:163 , GLN A:164 , HOH A:926BINDING SITE FOR RESIDUE SO4 A 903
13BC4SOFTWARETHR A:4 , ARG A:37 , ARG A:40 , ASN A:151BINDING SITE FOR RESIDUE SO4 A 904
14BC5SOFTWAREASN A:59 , VAL A:68 , PHE A:70BINDING SITE FOR RESIDUE ACT A 910

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:14 -A:33
2A:55 -A:72
3A:143 -A:158
4A:184 -A:201

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C9Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C9Z)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.NIGB_SAMNI305-431
434-559		  1-
A:129-254

(-) Exons   (0, 0)

(no "Exon" information available for 3C9Z)

(-) 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:257
 aligned with NIGB_SAMNI | P33183 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:257
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       
           NIGB_SAMNI   306 TSFTRNIVGRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQRWTFDSDDTIRSMGKCMTANGLNNGSNIVIFNCSTAAENAIKWEVPIDGSIINPSSGLVMTAPRAASRTILLLEDNIYAASQGWTVTNNVKPIVASIVGYKEMCLQSNGENNGVWMEDCEATSLQQQWALYGDRTIRVNSTRGLCVTTNGYNSKDLIIILKCQGLPSQRWFFNSDGAIVNPKSRHVMDVRASNVSLREIIIFPATGNPNQQWVTQVLP 562
               SCOP domains d3c9za1 A:1-128 automated matches                                                                                               d3c9za2 A:129-257 automated matches                                                                                               SCOP domains
               CATH domains 3c9zA01 A:1-130  [code=2.80.10.50, no name defined]                                                                               3c9zA02 A:131-255  [code=2.80.10.50, no name defined]                                                                        -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhheeee.hhh......eeee....hhhhheee.....eee..eeeeee......eeeee.....hhhhh.................eee..........eee....hhhhh.eee.....eeeeeehhhhheee........eee.....hhhh.eee.....eee..eeeeeeee........eeeee...hhhhh.ee.....ee......eeee.hhhhhhh.eeee....hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RICIN_B_LECTIN  PDB: - UniProt: 305-431                                                                                       --RICIN_B_LECTIN  PDB: A:129-254 UniProt: 434-559                                                                               --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9z A   1 TSFTRNIVGRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQRWTFDSDDTIRSMGKCMTANGLNNGSNIVIFNCSTAAENAIKWEVPIDGSIINPSSGLVMTAPRAASRTILLLEDNIYAASQGWTVTNNVKPIVASIVGYKEMCLQSNGENNGVWMEDCEATSLQQQWALYGDRTIRVNSTRGLCVTTNGYNSKDLIIILKCQGLPSQRWFFNSDGAIVNPKSRLVMDVRASNVSLREIIIFPATGNPNQQWVTQVLP 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C9Z)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NIGB_SAMNI | P33183)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NIGB_SAMNI | P33183: 3ca0 3ca1 3ca3 3ca4 3ca5 3ca6 3cah

(-) Related Entries Specified in the PDB File

3ca0 SAMBUCUS NIGRA AGGLUTININ II - HEXAGONAL CRYSTAL FORM
3ca1 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO GALACTOSE
3ca3 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO N-ACETYGALACTOSAMINE
3ca4 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO LACTOSE
3ca5 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO METHYL-GALACTOSE
3ca6 SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO TN ANTIGEN
3cah SAMBUCUS NIGRA AGGLUTININ II - TETRAGONAL CRYSTAL FORM - COMPLEXED TO FUCOSE