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(-) Description

Title :  BINDING DOMAIN OF BOTULINUM NEUROTOXIN DC IN COMPLEX WITH RAT SYNAPTOTAGMIN II
 
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 :  2.59
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (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-2
    Chains: D, E, F
    Engineered: YES
    Fragment: TOXIN BINDING SITE (UNP RESIDUES 40-60)
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTOTAGMIN II, SYTII
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:1251 , TRP A:1252 , PHE A:1253 , HIS A:1255BINDING SITE FOR RESIDUE SO4 A 1301
02AC2SOFTWAREARG A:1184 , ASN A:1254BINDING SITE FOR RESIDUE SO4 A 1302
03AC3SOFTWARELYS A:906 , TRP A:1065BINDING SITE FOR RESIDUE SO4 A 1303
04AC4SOFTWAREGLU A:1202 , LYS A:1205 , TYR A:1206 , LYS D:49 , LYS D:53BINDING SITE FOR RESIDUE SO4 A 1304
05AC5SOFTWARETYR B:1251 , TRP B:1252 , PHE B:1253 , HIS B:1255 , HOH B:1497BINDING SITE FOR RESIDUE SO4 B 1301
06AC6SOFTWAREARG B:1184 , ASN B:1254BINDING SITE FOR RESIDUE SO4 B 1302
07AC7SOFTWAREGLU A:923 , ASN A:924 , ARG B:1148 , ASN B:1154BINDING SITE FOR RESIDUE SO4 B 1303
08AC8SOFTWARETYR B:1090 , ASP B:1101 , ASP B:1155 , ARG B:1157 , ARG B:1159 , HOH B:1546BINDING SITE FOR RESIDUE SO4 B 1304
09AC9SOFTWARETYR C:1251 , TRP C:1252 , PHE C:1253 , HIS C:1255BINDING SITE FOR RESIDUE SO4 C 1301
10BC1SOFTWAREARG C:1103 , LYS C:1106 , HOH C:1489BINDING SITE FOR RESIDUE SO4 C 1302
11BC2SOFTWAREGLU C:1202 , LYS C:1205 , TYR C:1206 , LYS F:49 , LYS F:53BINDING SITE FOR RESIDUE SO4 C 1303
12BC3SOFTWARELYS B:1205 , TYR B:1206 , HOH B:1513 , LYS E:49 , LYS E:53BINDING SITE FOR RESIDUE SO4 E 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Phe A:901 -Pro A:902
2Phe B:901 -Pro B:902
3Asn B:943 -Lys B:944
4Phe C:901 -Pro C:902
5Asn C:922 -Glu C:923
6Glu C:923 -Asn C:924
7Asn D:56 -Glu D:57
8Asn E:56 -Glu E:57
9Asn F:56 -Glu F:57

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ISR)

(-) 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...hhhhh....eeeeeeeeeee........eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee.............eeeeeeee...eeeeee..eeeeeee...........eeeeeeee......eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.....eeeeee..eeeeee............eeeeeee............eeeeeeee..eeeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee.........eeeeeeeeee..hhhhh.hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4isr 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.......eeee.......eeeee.hhhhhhhhh..eeeeeeeeeee........eeeeeee....eeeeeee..eeeeeee.....eeeeeee.............eeeeeeee...eeeeee..eeeeeee...........eeeeeeee.....eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.....eeeeee..eeeeee............eeeeeee............eeeeeeee..eeeeeee..........eeeeeee..hhhhhhhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee.........eeeeeeeeee..hhhhh.hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4isr 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeeee....eee......eeeee...ee.......eeee.......eeeee....hhhhhhh.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
                4isr C  864 INDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPAS 1284
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      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   
                                                                                                                                                                                                                    1051|                                                                                                                                                                                                                                
                                                                                                                                                                                                                     1060                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:16
                                                 
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                4isr D   42 SQEDMFAKLKDKFFNE   57
                                    51      


Chain E from PDB  Type:PROTEIN  Length:16
                                                 
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                4isr E   42 SQEDMFAKLKDKFFNE   57
                                    51      


Chain F from PDB  Type:PROTEIN  Length:16
                                                 
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                4isr F   42 SQEDMFAKLKDKFFNE   57
                                    51
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

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 Related Entries

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

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        SYT2_RAT | P29101: 2nm1
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(-) Related Entries Specified in the PDB File

4isq SAME PROTEIN IN COMPLEX WITH HUMAN SYNAPTOTAGMIN 1