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(-) Description

Title :  RECEPTOR BINDING DOMAIN OF BOTULINUM NEUROTOXIN A IN COMPLEX WITH RAT SV2C
 
Authors :  G. Yao, S. Zhang, S. Mahrhold, K. Lam, D. Stern, K. Bagramyan, K. Perry, M A. Rummel, M. Dong, R. Jin
Date :  28 Apr 16  (Deposition) - 15 Jun 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Yao, S. Zhang, S. Mahrhold, K. H. Lam, D. Stern, K. Bagramyan, K. Perry, M. Kalkum, A. Rummel, M. Dong, R. Jin
N-Linked Glycosylation Of Sv2 Is Required For Binding And Uptake Of Botulinum Neurotoxin A.
Nat. Struct. Mol. Biol. V. 23 656 2016
PubMed-ID: 27294781  |  Reference-DOI: 10.1038/NSMB.3245

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
    Chains: A, C, E, G
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 872-1296
    Gene: BOTA, ATX, BNA
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: BONT/A,BONTOXILYSIN-A,BOTOX
 
Molecule 2 - SYNAPTIC VESICLE GLYCOPROTEIN 2C
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 455-577
    Gene: SV2C
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SYNAPTIC VESICLE PROTEIN 2C

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5JMC)

(-) Sites  (0, 0)

(no "Site" information available for 5JMC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JMC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:1138 -Pro A:1139
2Gly C:1138 -Pro C:1139
3Gly E:1138 -Pro E:1139
4Gly G:1138 -Pro G:1139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JMC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JMC)

(-) Exons   (0, 0)

(no "Exon" information available for 5JMC)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.eeeeee..eeee......eeee...eee.......eeee......eeee.......ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhh.................eeeeee......eeee........eeee....eeee...eeee......eeeeee............eeeeeeee..eeeeee............eeehhhhh.....eeeee.......eeeee.....eeeeeeeee....eeeeeehhhhh.......eeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5jmc A  868 GSHMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQRTLGCSWEFIPVDDGWGERPLLV 1298
                                   877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1169      1179      1189      1199      1209      1219      1233      1243      1253      1263      1278      1288      1298
                                                                                                                                                                                                                                                                                                                                  1165|                                                      1226|                                   1270|                      
                                                                                                                                                                                                                                                                                                                                   1168                                                       1231                                    1276                      


Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee......eeee..eee..eee..eee..eee..eee..eee..eee..eee..eee..eee....hhh.ee..eee.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                5jmc B  476 DKYANFSINFTMENQVHTGMEYDNGRFLGVKFKSVTFKDSVFKSCTFDDVTSVNTYFKNCTFIDTLFENTDFEPYKFIDSEFQNCSFLHNK  566
                                   485       495       505       515       525       535       545       555       565 


Chain C from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeeee..eeee......eeee...eee.......eeee.....eeeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhh.................eeeeee......eeee........eeee....eeee...eeee......eeeeee..........eeeeeee....eeeee.........ee.eeehhhhhh....eeeee.......eeeeee.....eeeeeeeeee..eeeeeeehhhhhh....eeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jmc C  868 GSHMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDTNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQTLGCSWEFIPVDDGWGERPLL 1297
                                   877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1171      1181      1191      1201      1211      1221      1234      1244      1254      1264     |1280      1290       
                                                                                                                                                                                                                                                                                                                                  1165|                                                      1228|                                  1270|                    
                                                                                                                                                                                                                                                                                                                                   1170                                                       1232                                   1277                    


Chain D from PDB  Type:PROTEIN  Length:92
                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeeee..eeeeeeee..eeeeeeee..eee..eee..eee..eee..eee..eee....hhh.ee..eee.eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                5jmc D  476 DKYANFSINFTMENQVHTGMEYDNGRFLGVKFKSVTFKDSVFKSCTFDDVTSVNTYFKNCTFIDTLFENTDFEPYKFIDSEFQNCSFLHNKT  567
                                   485       495       505       515       525       535       545       555       565  


Chain E from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhh.eeeeee..eeee......eeee...eeee..eeeeeeee.....eeeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee.............eeeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhh...................eeee......eeee........eeee....eeee...eeee.......eeeee..........eeeeeeeee..eeeeee.........ee.eeehhhhh.....eeeee........eeeee.....eeeeeeeee....eeeeee.......hhhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jmc E  868 GSHMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDTNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQRTLGCSWEFIPVDDGWGERPLL 1297
                                   877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1170      1180      1190      1200      1210      1220      1233      1243      1253      1263      1278      1288         
                                                                                                                                                                                                                                                                                                                                  1165|                                                       1228|                                  1270|                     
                                                                                                                                                                                                                                                                                                                                   1169                                                        1232                                   1276                     


Chain F from PDB  Type:PROTEIN  Length:92
                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eee..eeeeeeee..eee..eee..eee..eee..eee..eee..eee..eee....hhh.ee..eee.eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                5jmc F  476 DKYANFSINFTMENQVHTGMEYDNGRFLGVKFKSVTFKDSVFKSCTFDDVTSVNTYFKNCTFIDTLFENTDFEPYKFIDSEFQNCSFLHNKT  567
                                   485       495       505       515       525       535       545       555       565  


Chain G from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhh.eeeeee..eeee......eeee...eee......eeeee......eeee.hhhhh.ee....eeeeeeee.....hhhhh...eeeeeeee..eeeeeeee..eeeeeee.....eeeeeee.............eeeeeeee.....eeeee..eeeeee.......ee...eeeeeee.......eeeeeeeeee....hhhhhhhhhhhhh...................eeee......eeee........eeee....eeee...eeee.......eeeee...........eeeeeeee..eeeeee.........ee.eeehhhhh.....eeeee........eeeee.....eeeeeeeee....eeeeeehhhhhhhhhh.eeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jmc G  868 GSHMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDTNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQTLGCSWEFIPVDDGWGERPLLV 1298
                                   877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1170      1180      1190      1200      1210      1220      1233      1243      1253      1263      1279      1289         
                                                                                                                                                                                                                                                                                                                                  1165|                                                       1228|                                  1270|                     
                                                                                                                                                                                                                                                                                                                                   1169                                                        1232                                   1277                     


Chain H from PDB  Type:PROTEIN  Length:89
                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee......eeee..eee..eee..eee.eeee..eee..eeeeeeee..eee..eee..eeeee..hhh.ee..eee.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                5jmc H  476 DKYANFSINFTMENQVHTGMEYDNGRFLGVKFKSVTFKDSVFKSCTFDDVTSVNTYFKNCTFIDTLFENTDFEPYKFIDSEFQNCSFLH  564
                                   485       495       505       515       525       535       545       555
   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 5JMC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JMC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JMC)

(-) Gene Ontology  (32, 35)

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  Cis Peptide Bonds
    Gly A:1138 - Pro A:1139   [ RasMol ]  
    Gly C:1138 - Pro C:1139   [ RasMol ]  
    Gly E:1138 - Pro E:1139   [ RasMol ]  
    Gly G:1138 - Pro G:1139   [ RasMol ]  
 
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  5jmc
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  SV2C_RAT | Q9Z2I6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BXA1_CLOBO | P10845: 1uee 1xtf 1xtg 2ilp 2ima 2imb 2imc 2ise 2isg 2ish 2nyy 2nz9 2vu9 2vua 2w2d 3bok 3bon 3boo 3bta 3bwi 3c88 3c89 3c8a 3c8b 3dda 3ddb 3ds9 3fuo 3v0a 3v0b 3v0c 3zur 3zus 4ej5 4el4 4elc 4hev 4iqp 4jra 4zjx 5jlv 5tpb 5tpc 5vgv 5vgx

(-) Related Entries Specified in the PDB File

5jlv