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(-) Description

Title :  CRYSTAL STRUCTURE OF HA70 (HA3) SUBCOMPONENT OF CLOSTRIDIUM BOTULINUM TYPE C PROGENITOR TOXIN IN COMPLEX WITH ALPHA 2-3-SIALYLLACTOSE
 
Authors :  S. Yamashita, H. Yoshida, T. Tonozuka, A. Nishikawa, S. Kamitori
Date :  12 Apr 12  (Deposition) - 06 Jun 12  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Carbohydrate/Sugar Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamashita, H. Yoshida, N. Uchiyama, Y. Nakakita, S. Nakakita, T. Tonozuka, K. Oguma, A. Nishikawa, S. Kamitori
Carbohydrate Recognition Mechanism Of Ha70 From Clostridium Botulinum Deduced From X-Ray Structures In Complexes With Sialylated Oligosaccharides
Febs Lett. V. 586 2404 2012
PubMed-ID: 22684008  |  Reference-DOI: 10.1016/J.FEBSLET.2012.05.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMAGGLUTININ COMPONENTS HA-22/23/53
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-CRI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HA22-23(HA3A)
    Gene: HA-70
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: HEMAGGLUTININ COMPONENTS HA70, HA3
 
Molecule 2 - HEMAGGLUTININ COMPONENTS HA-22/23/53
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-CRI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HA53(HA3B)
    Gene: HA-70
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: HEMAGGLUTININ COMPONENTS HA70, HA3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MRD5Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3MRD15Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:102 , PHE A:103 , SER A:104 , HOH A:471 , SER B:241 , SER B:243 , VAL B:293BINDING SITE FOR RESIDUE MRD A 301
2AC2SOFTWAREASP A:58 , LEU A:59 , GLY A:100 , GLU A:102 , PRO B:247 , LEU B:289BINDING SITE FOR RESIDUE MRD A 302
3AC3SOFTWARELYS A:161 , PHE A:165 , ILE B:368 , ILE B:369 , HOH B:877BINDING SITE FOR RESIDUE MRD A 303
4AC4SOFTWAREILE B:264 , TYR B:269 , ASN B:317 , ASN B:374 , SER B:376 , HOH B:849 , HOH B:1028BINDING SITE FOR RESIDUE MRD B 704
5AC5SOFTWAREASN A:50 , GLU B:294 , PRO B:297 , LYS B:300 , ILE B:302 , ASP B:341 , HOH B:972 , HOH B:1027BINDING SITE FOR RESIDUE MRD B 705
6AC6SOFTWAREARG B:460 , ASP B:462 , ASP B:513 , ASN B:514 , TYR B:522 , TYR B:523 , THR B:524 , ARG B:525 , HOH B:801 , HOH B:803 , HOH B:804BINDING SITE FOR LINKED RESIDUES B 701 TO 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EN6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:423 -Pro B:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EN6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EN6)

(-) Exons   (0, 0)

(no "Exon" information available for 4EN6)

(-) Sequences/Alignments

Asymmetric 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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....ee.........eeeee...eeeeeee........eee.....hhhhhhhhhhhhh.hhhhhh....eeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeee......hhhhh.....ee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4en6 A  15 SINNVNLADGNYVVNRGDGWILSRQNQNLGGNISNNGCTAIVGDLRIRETATPYYYPTASFNEEYIKNNVQNVFANFTEASEIPIGFEFSKTAPSNKSLYMYLQYTYIRYEIIKVLQNTVTERAVLYVPSLGYVKSIEFNSEEQIDKNFYFTSQDKCILNEKFIYKKIDD 184
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184


Chain B from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eee.....eeeeeee....eeeeee.........eeee......hhhhhhhhhhhhhh.........eeeeeee......eeeeee..eeeeeeeee....eeeeeeeeee...eeeeee.................eee......eeeee.....eeee.......eeeee.hhhhhh..eeeee.....eeeeee........eeeee.......ee..........eeeeeee.......eeeeeee.....eeeee.........eeeeeee.hhhhhhh.eeeee..........eeeee......eeeeeee.........eeeeeeee...eeeeeeeeeeee..eeeeeeeeee.........eeee...eeeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4en6 B 204 QTILPYPNGLYVINKGDGYMRTNDKDLIGTLLIESSTSGSIIQPRLRNTTRPLFNTSNPTIFSQEYTEARLNDAFNIQLFNTSTTLFKFVEEAPTNKNISMKVYNTYEKYELINYQNGNIDDKAEYYLPSLGKCEVSDAPSPQAPVVETPVDQDGFIQTGPNENIIVGVINPSENIEEISTPIPDDYTYNIPTSIQNNACYVLFKVNTTGVYKITTKNNLPPLIIYEAIGSSNRNMNSNNLSNDNIKAIKYITGLNRSDAKSYLIVSLFKDKNYYIRIPQISSSTTSQLIFKRELGNISDLADSTVNILDNLNTSGTHYYTRQSPDVGNYISYQLTIPGDFNNIASSIFSFRTRNNQGIGTLYRLTESINGYNLITINNYSDLLNNVEPISLLNGATYIFRVKVTELNNYNIIFDAYRNS 623
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623
   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  (0, 0)

(no "SCOP Domain" information available for 4EN6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EN6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EN6)

(-) Gene Ontology  (2, 2)

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  HA70_CLOBO | P46085
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 Related Entries

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

UniProtKB/Swiss-Prot
        HA70_CLOBO | P46085: 2zoe 2zs6 4en7 4en8 4en9

(-) Related Entries Specified in the PDB File

2zoe THE SAME SUBCOMPONENT IN COMPLEX WITH N-ACETYLNEURAMIC ACID
2zs6 THE SAME SUBCOMPONENT WITHOUT LIGAND
4en7 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-3- SIALYLLACTOSAMINE
4en8 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-6- SIALYLLACTOSE
4en9 THE SAME SUBCOMPONENT IN COMPLEX WITH ALPHA 2-6- SIALYLLACTOSAMINE