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(-) Description

Title :  BINDING DOMAIN OF BOTULINUM NEUROTOXIN DC IN COMPLEX WITH HUMAN SYNAPTOTAGMIN I
 
Authors :  R. P. -A. Berntsson, L. Peng, L. M. Svensson, M. Dong, P. Stenmark
Date :  17 Jan 13  (Deposition) - 14 Aug 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Membrane Binding, Synaptotagmin And Ganglioside Binding, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Berntsson, L. Peng, L. M. Svensson, M. Dong, P. Stenmark
Crystal Structures Of Botulinum Neurotoxin Dc In Complex With Its Protein Receptors Synaptotagmin I And Ii.
Structure V. 21 1602 2013
PubMed-ID: 23932591  |  Reference-DOI: 10.1016/J.STR.2013.06.026

(-) Compounds

Molecule 1 - NEUROTOXIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HC DOMAIN (UNP RESIDUES 864-1285)
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
 
Molecule 2 - SYNAPTOTAGMIN-1
    Chains: D, E, F
    Engineered: YES
    Fragment: TOXIN BINDING SITE (UNP RESIDUES 33-53)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SYNAPTOTAGMIN I, SYTI, P65
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A    F
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2SO420Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 3 (2, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:1251 , TRP A:1252 , PHE A:1253 , HIS A:1255 , HOH A:1423BINDING SITE FOR RESIDUE SO4 A 1301
02AC2SOFTWAREARG A:1184 , SER A:1244 , ASN A:1254 , HOH A:1492BINDING SITE FOR RESIDUE SO4 A 1302
03AC3SOFTWARESER A:1239 , ILE A:1240 , TYR A:1243 , LEU A:1270BINDING SITE FOR RESIDUE SO4 A 1303
04AC4SOFTWARELYS A:1205 , TYR A:1206 , LYS F:42 , LYS F:46BINDING SITE FOR RESIDUE SO4 A 1304
05AC5SOFTWARETHR A:1216 , PHE A:1217BINDING SITE FOR RESIDUE SO4 A 1305
06AC6SOFTWAREGLU A:1140 , GLY A:1141BINDING SITE FOR RESIDUE SO4 A 1306
07AC7SOFTWARELYS A:995 , LYS A:1002 , TYR A:1097 , VAL A:1113 , TYR A:1219BINDING SITE FOR RESIDUE GOL A 1307
08AC8SOFTWARESER A:1242 , GLU A:1256 , LEU A:1258 , HOH A:1496BINDING SITE FOR RESIDUE GOL A 1308
09AC9SOFTWAREPRO A:902 , TRP A:1003 , ARG A:1067 , GLN A:1089 , LYS A:1095 , GLY A:1099 , TYR A:1220 , HOH A:1474BINDING SITE FOR RESIDUE GOL A 1309
10BC1SOFTWAREHIS A:1266 , SER A:1269BINDING SITE FOR RESIDUE GOL A 1310
11BC2SOFTWAREARG B:1103 , LYS B:1106 , HOH B:1480BINDING SITE FOR RESIDUE SO4 B 1301
12BC3SOFTWARESER B:1239 , ILE B:1240 , TYR B:1243BINDING SITE FOR RESIDUE SO4 B 1302
13BC4SOFTWARELYS B:1205 , TYR B:1206 , LYS E:46BINDING SITE FOR RESIDUE SO4 B 1303
14BC5SOFTWARETHR B:1156 , HOH B:1434BINDING SITE FOR RESIDUE SO4 B 1304
15BC6SOFTWARELYS B:995 , TYR B:1097 , VAL B:1113 , MET B:1116BINDING SITE FOR RESIDUE SO4 B 1305
16BC7SOFTWAREASN A:924 , LYS A:1040 , ARG B:1148 , GLY B:1151BINDING SITE FOR RESIDUE SO4 B 1306
17BC8SOFTWAREHIS B:1266 , TYR B:1267 , ALA B:1268 , SER B:1269BINDING SITE FOR RESIDUE GOL B 1307
18BC9SOFTWAREARG C:1103 , LYS C:1106BINDING SITE FOR RESIDUE SO4 C 1301
19CC1SOFTWARETYR C:1251 , TRP C:1252 , PHE C:1253 , HIS C:1255BINDING SITE FOR RESIDUE SO4 C 1302
20CC2SOFTWARELYS C:1205 , TYR C:1206 , LYS D:42 , LYS D:46BINDING SITE FOR RESIDUE SO4 C 1303
21CC3SOFTWARETHR C:1216 , PHE C:1217BINDING SITE FOR RESIDUE SO4 C 1304
22CC4SOFTWARESER C:1239 , ILE C:1240 , TYR C:1243 , VAL C:1261 , LEU C:1270 , SER C:1275BINDING SITE FOR RESIDUE SO4 C 1305
23CC5SOFTWAREILE C:900 , ASP C:1155 , ARG C:1157BINDING SITE FOR RESIDUE SO4 C 1306
24CC6SOFTWAREARG C:1148 , ILE C:1149 , THR C:1153BINDING SITE FOR RESIDUE SO4 C 1307
25CC7SOFTWARELYS C:995 , TYR C:1097 , MET C:1116 , ASP C:1218 , TYR C:1219BINDING SITE FOR RESIDUE SO4 C 1308
26CC8SOFTWAREPHE A:901 , TYR A:1090 , ASP A:1101 , ARG A:1157 , ARG A:1159 , HOH A:1485 , ASN C:928 , HOH C:1437BINDING SITE FOR RESIDUE GOL C 1309
27CC9SOFTWAREASN B:928 , PHE C:901 , TYR C:1090 , ASP C:1101 , ARG C:1157 , ARG C:1159 , HOH C:1468BINDING SITE FOR RESIDUE GOL C 1310
28DC1SOFTWARETYR C:1267 , ALA C:1268 , SER C:1269BINDING SITE FOR RESIDUE GOL C 1311

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Phe A:901 -Pro A:902
2Asn A:943 -Lys A:944
3Phe B:901 -Pro B:902
4Asn B:943 -Lys B:944
5Phe C:901 -Pro C:902
6Asn C:943 -Lys C:944
7Glu C:1032 -Leu C:1033

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ISQ)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhh.eeeeeee....eee......eeeee...ee.......eeee.......eeeee..hhhhhh....eeeeeeeeeee........eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee.............eeeeeeee...eeeeee..eeeeeee...........eeeeeeee......eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeeee..eeeeee............eeeeeee............eeeeeeee..eeeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee.........eeeeeeeeee........hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4isq A  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
                                   872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280    
                                                                                                                                                                                                                     1051|                                                                                                                                                                                                                                
                                                                                                                                                                                                                      1060                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeee....eee......eeeee...ee.......eee........eeeee.hhhhhhhhh..eeeeeeeeeee........eeeeeee....eeeeeee..eeeeeeeee..eeeeeeee.............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
                4isq B  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
                                   872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281   
                                                                                                                                                                                                                    1050|                                                                                                                                                                                                                                
                                                                                                                                                                                                                     1060                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhh.eeeeeee....eee......eeeee...ee.......eeee.......eeeee...hhhhhhhh.eeeeeeeeeee........eeeeeee....eeeeeee..eeeeeee.....eeeeeee.............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
                4isq C  863 SINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
                                   872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280    
                                                                                                                                                                                                                     1051|                                                                                                                                                                                                                                
                                                                                                                                                                                                                      1060                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4isq D   36 KEDAFSKLKEKFMNE   50
                                    45     


Chain E from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4isq E   36 KEDAFSKLKEKFMNE   50
                                    45     


Chain F from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                4isq F   36 KEDAFSKLKEKFMNE   50
                                    45
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
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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 4ISQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (71, 71)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT1_HUMAN | P21579: 2k45 2k4a 2k8m 2ki6 2lha 2n1t 2r83 3f00 3f01 3f04 3f05 4v11
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        Q9LBR1_CLOBO | Q9LBR1: 3azv 3azw 3n7l 3n7m 4fvv 4isr

(-) Related Entries Specified in the PDB File

4isr