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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BOTULINUM NEUROTOXIN A RECEPTOR-BINDING DOMAIN IN COMPLEX WITH THE LUMINAL DOMAIN OF SV2C
 
Authors :  R. M. Benoit, D. Frey, M. M. Wieser, R. Jaussi, G. F. X. Schertler, G. Capi R. A. Kammerer
Date :  21 Mar 13  (Deposition) - 20 Nov 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Beta-Helix, Vesicles, Lumen, Toxin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Benoit, D. Frey, M. Hilbert, J. T. Kevenaar, M. M. Wieser, C. U. Stirnimann, D. Mcmillan, T. Ceska, F. Lebon, R. Jaussi, M. O. Steinmetz, G. F. Schertler, C. C. Hoogenraad, G. Capitani, R. A. Kammerer
Structural Basis For Recognition Of Synaptic Vesicle Protei 2C By Botulinum Neurotoxin A.
Nature V. 505 108 2014
PubMed-ID: 24240280  |  Reference-DOI: 10.1038/NATURE12732

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE A
    Chains: A, B
    EC Number: 3.4.24.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BOTA, ATX, BNA
    Organism Scientific: CLOSTRIDIUM BOTULINUM
    Organism Taxid: 1491
    Synonym: BONT/A, BONTOXILYSIN-A, BOTOX, BOTULINUM NEUROTOXIN A LIGHT CHAIN, BOTULINUM NEUROTOXIN A HEAVY CHAIN
 
Molecule 2 - SYNAPTIC VESICLE GLYCOPROTEIN 2C
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SV2C, KIAA1054
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:1100BINDING SITE FOR RESIDUE CL A 1301
2AC2SOFTWAREARG A:1034BINDING SITE FOR RESIDUE CL A 1302
3AC3SOFTWAREGLU A:1210BINDING SITE FOR RESIDUE CL A 1303
4AC4SOFTWARELEU A:1097 , LYS A:1098BINDING SITE FOR RESIDUE CL A 1304
5AC5SOFTWARESER A:1002 , TYR A:1010 , NA A:1306BINDING SITE FOR RESIDUE CL A 1305
6AC6SOFTWARESER A:1002 , SER A:1008 , CL A:1305BINDING SITE FOR RESIDUE NA A 1306
7AC7SOFTWAREASP A:1099 , TYR A:1104 , TYR A:1111BINDING SITE FOR RESIDUE NA A 1307
8AC8SOFTWARETYR A:980 , GLN A:1003 , MET A:1004BINDING SITE FOR RESIDUE CL A 1308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:1044 -Gly A:1045
2Gly A:1138 -Pro A:1139
3Leu B:1044 -Gly B:1045
4Gly B:1138 -Pro B:1139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JRA)

(-) 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jraa1 A:876-1079 automated matches                                                                                                                                                                        d4jraa2 A:1080-1296 automated matches                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeee......eeee....eee..eeeeeeee......eeee.......ee....eeeeeeee.....hhhhh...eeeeeee....eeeeeee..eeeeeee.....eeeeeee..............eeeeeee....eeeeee..eeeeeee......eeeeeeeeeeee.......eeeeeeeeee....hhhhhhhhhhhh....................eeee......eeee........eeee....eeee...eeee......eeeeee............eeeeeeee..eeeeee.........ee.eeehhhhh......eee..........eeee.....eeeeeeeeee..eeeeeee.hhhhhh..........eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jra A  876 TSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL 1296
                                   885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165  ||  1177      1187      1197      1207      1217      1227|     1240      1250      1260      1270      1280      1290      
                                                                                                                                                                                                                                                                                                                             1168|                                                    1227|                                                                 
                                                                                                                                                                                                                                                                                                                              1171                                                     1231                                                                 


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4jrab1 B:875-1079 automated matches                                                                                                                                                                         d4jrab2 B:1080-1296 automated matches                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeee......eeee....ee.......eeee......eeee.......ee....eeeeeeee.....hhhhh...eeeeeee....eeeeeee..eeeeee........eeeee..............eeeeeee....eeeeee..eeeeeee......ee...eeeeeee.......eeeee.eee.....hhhhhhhhhhhhh...................eeee......eeee........eeee....eeee...eeee.......eeeee...........eeeeeeee..eeeeeee........eeeeeehhhhh.....eeee...........eeee.....eeeeeeeeee..eeeeeehhhhhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jra B  875 NTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQTNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERLGCSWEFIPVDDGWGERPL 1296
                                   884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164  ||  1177      1187      1197      1207      1217      1227 ||   1239      1249      1259      1269   || 1283      1293   
                                                                                                                                                                                                                                                                                                                             1167|                                                      1229|                                     1273|                  
                                                                                                                                                                                                                                                                                                                              1171                                                       1232                                      1278                  


Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.......eee.......eee...ee..eee..eee..eee...ee..eee..eee....hhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                4jra C  479 ANFTITMENQIHTGMEYDNGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFKNCSFF  563
                                || 490       500       510       520       530       540       550       560   
                              483|                                                                             
                               486                                                                             


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eee..eee.eeeeeeeee..eee..eee..eee..eee..eee..eee..eee..eee....hhh.ee..eee.eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                4jra D  473 VERDKYANFTINFTMENQIHTGMEYDNGRFIGVKFKSVTFKDSVFKSCTFEDVTSVNTYFKNCTFIDTVFDNTDFEPYKFIDSEFKNCSFFHN  565
                                   482       492       502       512       522       532       542       552       562
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 35)

Asymmetric Unit(hide GO term definitions)

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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 4zjx 5jlv 5jmc 5tpb 5tpc 5vgv 5vgx
        SV2C_HUMAN | Q496J9: 5jlv 5moy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JRA)