Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CELL ENTRY OF BOTULINUM NEUROTOXIN TYPE C IS DEPENDENT UPON INTERACTION WITH TWO GANGLIOSIDE MOLECULES
 
Authors :  J. Strotmeier, S. Gu, S. Jutzi, S. Mahrhold, J. Zhou, A. Pich, H. Bigalke A. Rummel, R. Jin, T. Binz
Date :  17 Mar 11  (Deposition) - 08 Jun 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Botulinum Toxins, Gangliosides, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Strotmeier, S. Gu, S. Jutzi, S. Mahrhold, J. Zhou, A. Pich, T. Eichner, H. Bigalke, A. Rummel, R. Jin, T. Binz
The Biological Activity Of Botulinum Neurotoxin Type C Is Dependent Upon Novel Types Of Ganglioside Binding Sites.
Mol. Microbiol. V. 81 143 2011
PubMed-ID: 21542861  |  Reference-DOI: 10.1111/J.1365-2958.2011.07682.X

(-) Compounds

Molecule 1 - BOTULINUM NEUROTOXIN TYPE C1
    ChainsA, B
    EC Number3.4.24.69
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentHCC DOMAIN, UNP RESIDUES 867-1291
    Organism ScientificCLOSTRIDIUM BOTULINUM
    Organism Taxid1491
    SynonymBONT/C1, BONTOXILYSIN-C1, BOTULINUM NEUROTOXIN C1 HEAVY CHAIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1SIA2Ligand/IonO-SIALIC ACID
2SLB2Ligand/Ion5-N-ACETYL-BETA-D-NEURAMINIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1SIA1Ligand/IonO-SIALIC ACID
2SLB1Ligand/Ion5-N-ACETYL-BETA-D-NEURAMINIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1SIA1Ligand/IonO-SIALIC ACID
2SLB1Ligand/Ion5-N-ACETYL-BETA-D-NEURAMINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:309 , HOH B:504 , HOH B:722 , HOH B:775 , TYR B:1125 , ALA B:1126 , ASN B:1127 , SER B:1128 , ARG B:1129 , TYR B:1146BINDING SITE FOR RESIDUE SLB B 6875
2AC2SOFTWAREHOH A:181 , HOH A:662 , HOH A:730 , TYR A:1125 , ALA A:1126 , ASN A:1127 , SER A:1128 , ARG A:1129 , TYR A:1146 , TYR A:1179BINDING SITE FOR RESIDUE SLB A 6875
3AC3SOFTWAREHOH B:163 , HOH B:370 , HOH B:484 , TYR B:1169 , ASP B:1171 , ASN B:1180 , GLN B:1206 , THR B:1207 , LYS B:1208 , ILE B:1210BINDING SITE FOR RESIDUE SIA B 6859
4AC4SOFTWAREHOH A:206 , HOH A:305 , HOH A:339 , HOH A:576 , TYR A:1169 , ASP A:1171 , ASN A:1180 , GLN A:1206 , THR A:1207 , LYS A:1208BINDING SITE FOR RESIDUE SIA A 6859

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R4S)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:905 -Pro A:906
2Asn A:947 -Lys A:948
3Thr A:1056 -Gly A:1057
4Phe B:905 -Pro B:906
5Asn B:947 -Lys B:948
6Asp B:1055 -Thr B:1056

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R4S)

(-) Exons   (0, 0)

(no "Exon" information available for 3R4S)

(-) 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:424
 aligned with BXC1_CLOBO | P18640 from UniProtKB/Swiss-Prot  Length:1291

    Alignment length:428
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283        
          BXC1_CLOBO    864 YFNNINDSKILSLQNRKNTLVDTSGYNAEVSEEGDVQLNPIFPFDFKLGSSGEDRGKVIVTQNENIVYNSMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNEDSEQSINFSYDISNNAPGYNKWFFVTVTNNMMGNMKIYINGKLIDTIKVKELTGINFSKTITFEINKIPDTGLITSDSDNINMWIRDFYIFAKELDGKDINILFNSLQYTNVVKDYWGNDLRYNKEYYMVNIDYLNRYMYANSRQIVFNTRRNNNDFNEGYKIIIKRIRGNTNDTRVRGGDILYFDMTINNKAYNLFMKNETMYADNHSTEDIYAIGLREQTKDINDNIIFQIQPMNNTYYYASQIFKSNFNGENISGICSIGTYRFRLGGDWYRHNYLVPTVKQGNYASLLESTSTHWGFVPVSE 1291
               SCOP domains d3r4sa1 A:864-1093 automated matches                                                                                                                                                                                                  d3r4sa2 A:1094-1291 automated matches                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhheeeeeee....eee......eeeee...ee.......eeee.......eeeee.hhhhhhhhh..eeeeeeeeeee........eeeeeeee..eeeeeeee..eeeeeeeee..eeeeeeee.hhhhh.......eeeeeeee...eeeeee..eeeeeee...........eeeeeeee.....----.....eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeeee..eeeeee............eeeeeee............eeeeeeee..eeeeeee..............eeeeeeee.....hhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee........eeeeeeeee..hhhhhh.hhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r4s A  864 SMANINDSKILSLQNRKNTLVDTSGYNAEVSEEGDVQLNPIFPFDFKLGSSGEDRGKVIVTQNENIVYNSMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNEDSEQSINFSYDISNNAPGYNKWFFVTVTNNMMGNMKIYINGKLIDTIKVKELTGINFSKTITFEINKIPDTG----DSDNINMWIRDFYIFAKELDGKDINILFNSLQYTNVVKDYWGNDLRYNKEYYMVNIDYLNRYMYANSRQIVFNTRRNNNDFNEGYKIIIKRIRGNTNDTRVRGGDILYFDMTINNKAYNLFMKNETMYADNHSTEDIYAIGLREQTKDINDNIIFQIQPMNNTYYYASQIFKSNFNGENISGICSIGTYRFRLGGDWYRHNYLVPTVKQGNYASLLESTSTHWGFVPVSE 1291
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053   |  1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283        
                                                                                                                                                                                                                          1057 1062                                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:424
 aligned with BXC1_CLOBO | P18640 from UniProtKB/Swiss-Prot  Length:1291

    Alignment length:428
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283        
          BXC1_CLOBO    864 YFNNINDSKILSLQNRKNTLVDTSGYNAEVSEEGDVQLNPIFPFDFKLGSSGEDRGKVIVTQNENIVYNSMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNEDSEQSINFSYDISNNAPGYNKWFFVTVTNNMMGNMKIYINGKLIDTIKVKELTGINFSKTITFEINKIPDTGLITSDSDNINMWIRDFYIFAKELDGKDINILFNSLQYTNVVKDYWGNDLRYNKEYYMVNIDYLNRYMYANSRQIVFNTRRNNNDFNEGYKIIIKRIRGNTNDTRVRGGDILYFDMTINNKAYNLFMKNETMYADNHSTEDIYAIGLREQTKDINDNIIFQIQPMNNTYYYASQIFKSNFNGENISGICSIGTYRFRLGGDWYRHNYLVPTVKQGNYASLLESTSTHWGFVPVSE 1291
               SCOP domains d3r4sb1 B:864-1093 automated matches                                                                                                                                                                                                  d3r4sb2 B:1094-1291 automated matches                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------Toxin_R_bind_N-3r4sB01 B:880-1080                                                                                                                                                                        --------Toxin_R_bind_C-3r4sB03 B:1089-1291                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ----------------Toxin_R_bind_N-3r4sB02 B:880-1080                                                                                                                                                                        --------Toxin_R_bind_C-3r4sB04 B:1089-1291                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .hhhhhh.eeeeeeee..eeee......eeeee...ee.......eeee.......eeeee.hhhhhhh....eeeeeeeeeee........eeeeeeee..eeeeeeee..eeeeeeeee..eeeeeeee.hhhhh.......eeeeeeee...eeeeee..eeeeeee...........eeeeeeee.....----.....eeeeeeeeee....hhhhhhhhhhhh..................eeeeee.hhh.eeeeee..eeeeee............eeeeeee............eeeeeeee..eeeeeee..............eeeeeeee.....hhhh.eeeeeee....eeeeeeee......eeeeeeeeeeee........eeeeeeeee..hhhhhh.hhhh.eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r4s B  864 SMANINDSKILSLQNRKNTLVDTSGYNAEVSEEGDVQLNPIFPFDFKLGSSGEDRGKVIVTQNENIVYNSMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNEDSEQSINFSYDISNNAPGYNKWFFVTVTNNMMGNMKIYINGKLIDTIKVKELTGINFSKTITFEINKIPDTG----DSDNINMWIRDFYIFAKELDGKDINILFNSLQYTNVVKDYWGNDLRYNKEYYMVNIDYLNRYMYANSRQIVFNTRRNNNDFNEGYKIIIKRIRGNTNDTRVRGGDILYFDMTINNKAYNLFMKNETMYADNHSTEDIYAIGLREQTKDINDNIIFQIQPMNNTYYYASQIFKSNFNGENISGICSIGTYRFRLGGDWYRHNYLVPTVKQGNYASLLESTSTHWGFVPVSE 1291
                                   873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053   |  1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283        
                                                                                                                                                                                                                          1057 1062                                                                                                                                                                                                                                     

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R4S)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BXC1_CLOBO | P18640)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051609    inhibition of neurotransmitter uptake    Any process that prevents the activation of the directed movement of a neurotransmitter into a cell.
    GO:0033619    membrane protein proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains.
    GO:0045955    negative regulation of calcium ion-dependent exocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044164    host cell cytosol    The part of the host cell cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0044156    host cell junction    A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0044231    host cell presynaptic membrane    A specialized area of membrane of the host axon terminal that faces the plasma membrane of the host neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many host synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0044221    host cell synapse    The junction between a nerve fiber of one host neuron and another host neuron or muscle fiber or glial cell; the site of interneuronal communication.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SLB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:947 - Lys A:948   [ RasMol ]  
    Asn B:947 - Lys B:948   [ RasMol ]  
    Asp B:1055 - Thr B:1056   [ RasMol ]  
    Phe A:905 - Pro A:906   [ RasMol ]  
    Phe B:905 - Pro B:906   [ RasMol ]  
    Thr A:1056 - Gly A:1057   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3r4s
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BXC1_CLOBO | P18640
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.69
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BXC1_CLOBO | P18640
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BXC1_CLOBO | P186402qn0 3deb 3n7k 3r4u

(-) Related Entries Specified in the PDB File

3r4u