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(-) Description

Title :  CRYSTAL STRUCTURE OF HCR/D-SA-GBL1/C
 
Authors :  Z. Fu, A. Karalewitz, M. R. Baldwin, J. -J. P. Kim, J. T. Barbieri
Date :  29 Jun 12  (Deposition) - 24 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Botulinum Toxin, Ganglioside Bing Loop, Ganglioside, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Karalewitz, Z. Fu, M. R. Baldwin, J. J. Kim, J. T. Barbieri
Botulinum Neurotoxin Serotype C Associates With Dual Ganglioside Receptors To Facilitate Cell Entry.
J. Biol. Chem. V. 287 40806 2012
PubMed-ID: 23027864  |  Reference-DOI: 10.1074/JBC.M112.404244

(-) Compounds

Molecule 1 - NEUROTOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR BINDING DOMAIN, UNP RESIDUES 862-1285
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SIA1Ligand/IonO-SIALIC ACID
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SIA-1Ligand/IonO-SIALIC ACID
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SIA1Ligand/IonO-SIALIC ACID
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:1119 , SER A:1121 , ASN A:1130 , ASP A:1250 , TRP A:1251 , TYR A:1252 , HIS A:1254BINDING SITE FOR RESIDUE SO4 A 1301
2AC2SOFTWARELYS A:1123 , GLY A:1124 , GLY A:1248BINDING SITE FOR RESIDUE SO4 A 1302
3AC3SOFTWARESER A:1183 , ARG A:1184 , ARG A:1246 , ARG A:1253BINDING SITE FOR RESIDUE SO4 A 1303
4AC4SOFTWAREILE A:900 , ASP A:1155 , ARG A:1157 , PHE B:972BINDING SITE FOR RESIDUE GOL A 1304
5AC5SOFTWAREHOH B:1520BINDING SITE FOR RESIDUE GOL B 1401
6AC6SOFTWAREILE A:1263 , GLU A:1264 , GLY B:1249 , ASP B:1250 , TRP B:1251 , TYR B:1252 , HOH B:1523BINDING SITE FOR RESIDUE GOL B 1402
7AC7SOFTWARETYR B:1115 , ILE B:1240 , GLY B:1241 , SER B:1242 , TYR B:1243 , LEU B:1269 , SER B:1274BINDING SITE FOR RESIDUE SIA B 1403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:901 -Pro A:902
2Phe B:901 -Pro B:902

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FVV)

(-) 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:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4fvva1 A:863-1076 automated matches                                                                                                                                                                         d4fvva2 A:1077-1283 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeee..eeee......eeeee...ee.......eeee.......eeeee....hhhhhhh.eeeeeeeeeee........eeeeeee....eeeeee...eeeeeee.....eeeeeee.hhhhh.......eeeeeeee...eeeeee..eeeeeee..........eeeeeeee......eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeeee..eeeeee............eeeeeee............eeeeeee....eeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee........eeeeeeeeee........hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fvv A  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKLTGINFSKTITFQMNKIPSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFRLGGDWYRHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1283
                                   872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1033      1043      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281  
                                                                                                                                                                                                 1031|             1050|                                                                                                                                                                                                                                
                                                                                                                                                                                                  1033              1059                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4fvvb1 B:863-1076 automated matches                                                                                                                                                                            d4fvvb2 B:1077-1283 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeee....eee......eeeee...ee.......eeee.......eeeee...hhhhhhhh.eeeeeeeeeee........eeeeeee....eeeeeee..eeeeeee......eeeeee.............eeeeeeee...eeeeee..eeeeeee..........eeeeeeee.........eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeeee..eeeeee............eeeeeee............eeeeeee....eeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee........eeeeeeeeee........hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fvv B  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKLTGINFSKTITFQMNKIPNTGSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFRLGGDWYRHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1283
                                   872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1033      1043      1053|     1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278     
                                                                                                                                                                                                 1031|                1053|                                                                                                                                                                                                                                
                                                                                                                                                                                                  1033                 1059
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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        Q9LBR1_CLOBO | Q9LBR1: 3azv 3azw 3n7l 3n7m 4isq 4isr

(-) Related Entries Specified in the PDB File

3n7l THE LOOP OF 9 RESIDUES, KLGDDYWFN IS REPLACED BY 8 RESIDUES, RLGGDWYR