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(-) Description

Title :  CRYSTAL STRUCTURE OF TAIWAN COBRA CARDIOTOXIN A3 COMPLEXED WITH SULFOGALACTOCERAMIDE
 
Authors :  C. -H. Wang, J. -H. Liu, P. -L. Wu, S. -C. Lee, C. -D. Hsiao, W. -G. Wu
Date :  12 Jan 05  (Deposition) - 28 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cardiotoxin, Cobra Cardiotoxin, Sulfogalactoceramide Sulfatide, Glycosphingolipid, Membrane Pore Formation, Cytolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. -H. Wang, J. -H. Liu, S. -C. Lee, C. -D. Hsiao, W. -G. Wu
Glycosphingolipid-Facilitated Membrane Insertion And Internalization Of Cobra Cardiotoxin: The Sulfatide/Cardiotoxin Complex Structure In A Membrane-Like Environment Suggests A Lipid- Dependent Cell-Penetrating Mechanism For Membrane Binding Polypeptides.
J. Biol. Chem. V. 281 656 2006
PubMed-ID: 16263708  |  Reference-DOI: 10.1074/JBC.M507880200

(-) Compounds

Molecule 1 - CYTOTOXIN 3
    ChainsA, B
    OrganVENOM GLAND
    Organism CommonCHINESE COBRA
    Organism ScientificNAJA ATRA
    Organism Taxid8656
    SynonymCARDIOTOXIN 3, CTX-3, CARDIOTOXIN ANALOG III, CTX IIICARDIOTOXIN 3

 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, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1C1011Ligand/IonHEXAETHYLENE GLYCOL MONODECYL ETHER
2SFT1Ligand/IonSULFOGALACTOCERAMIDE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1C106Ligand/IonHEXAETHYLENE GLYCOL MONODECYL ETHER
2SFT1Ligand/IonSULFOGALACTOCERAMIDE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1C105Ligand/IonHEXAETHYLENE GLYCOL MONODECYL ETHER
2SFT-1Ligand/IonSULFOGALACTOCERAMIDE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:12 , PRO A:15 , LYS A:18 , TYR A:22 , LYS A:35 , ARG A:36 , GLY A:37 , CYS A:38 , VAL A:41 , CYS A:42 , PRO A:43 , C10 A:1067 , HOH A:2006 , HOH A:2044 , LYS B:2 , ALA B:16 , GLY B:17 , LYS B:18 , ASP B:40 , PRO B:43 , LYS B:44 , C10 B:1061 , HOH B:2016 , HOH B:2017 , HOH B:2045BINDING SITE FOR RESIDUE SFT A1061
02AC2SOFTWAREVAL A:7 , TYR A:11 , LYS A:12 , THR A:13 , PHE B:10 , TYR B:11BINDING SITE FOR RESIDUE C10 A1062
03AC3SOFTWARETYR A:11 , LYS A:44 , SER A:46 , LEU A:47 , HOH A:2045 , HOH A:2046 , LEU B:6 , VAL B:7BINDING SITE FOR RESIDUE C10 A1063
04AC4SOFTWAREASN A:4 , PRO A:8 , VAL A:27 , PRO A:30 , LYS A:50 , ARG A:58 , HOH A:2038 , HOH A:2039 , HOH A:2047 , VAL B:32 , C10 B:1063BINDING SITE FOR RESIDUE C10 A1064
05AC5SOFTWAREPRO A:8 , ARG A:36 , HOH A:2048BINDING SITE FOR RESIDUE C10 A1065
06AC6SOFTWARELYS A:23 , LYS A:31 , VAL A:52BINDING SITE FOR RESIDUE C10 A1066
07AC7SOFTWARESFT A:1061 , HOH A:2049BINDING SITE FOR RESIDUE C10 A1067
08AC8SOFTWAREMET A:24 , LYS A:35 , ILE A:39 , PRO A:43 , TYR A:51 , SFT A:1061 , LYS B:12 , PRO B:15 , LYS B:18 , TYR B:22 , LYS B:35 , CYS B:38 , PRO B:43 , TYR B:51 , HOH B:2017 , HOH B:2020 , HOH B:2045 , HOH B:2046BINDING SITE FOR RESIDUE C10 B1061
09AC9SOFTWAREVAL A:32 , VAL A:34 , MET B:26 , VAL B:27 , ALA B:28 , LYS B:31 , LEU B:48 , C10 B:1063BINDING SITE FOR RESIDUE C10 B1062
10BC1SOFTWAREC10 A:1064 , LEU B:6 , LYS B:23 , LYS B:31 , ARG B:36 , LYS B:50 , C10 B:1062 , HOH B:2025 , HOH B:2034BINDING SITE FOR RESIDUE C10 B1063
11BC2SOFTWAREPHE B:25 , PRO B:30 , HOH B:2048BINDING SITE FOR RESIDUE C10 B1064
12BC3SOFTWARELEU B:20 , ASN B:55 , THR B:56 , HOH B:2036 , HOH B:2037 , HOH B:2049BINDING SITE FOR RESIDUE C10 B1065

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:3 -A:21
2A:14 -A:38
3A:42 -A:53
4A:54 -A:59
5B:3 -B:21
6B:14 -B:38
7B:42 -B:53
8B:54 -B:59

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BHI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BHI)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA4_NAJKA58-78
 
  2A:37-57
B:37-57
3SA3_NAJAT58-78
 
  2A:37-57
B:37-57
3SA3_NAJSP58-78
 
  2A:37-57
B:37-57
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA4_NAJKA58-78
 
  1A:37-57
-
3SA3_NAJAT58-78
 
  1A:37-57
-
3SA3_NAJSP58-78
 
  1A:37-57
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA4_NAJKA58-78
 
  1-
B:37-57
3SA3_NAJAT58-78
 
  1-
B:37-57
3SA3_NAJSP58-78
 
  1-
B:37-57

(-) Exons   (0, 0)

(no "Exon" information available for 2BHI)

(-) 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:60
 aligned with 3SA3_NAJAT | P60301 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJAT   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhia_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiA00 A:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi A  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain A from PDB  Type:PROTEIN  Length:60
 aligned with 3SA3_NAJSP | P60302 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJSP   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhia_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiA00 A:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------SNAKE_TOXIN          --- PROSITE (3)
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi A  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain A from PDB  Type:PROTEIN  Length:60
 aligned with 3SA4_NAJKA | P60303 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA4_NAJKA   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhia_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiA00 A:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------SNAKE_TOXIN          --- PROSITE (2)
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi A  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with 3SA3_NAJAT | P60301 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJAT   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhib_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiB00 B:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi B  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with 3SA3_NAJSP | P60302 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJSP   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhib_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiB00 B:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------SNAKE_TOXIN          --- PROSITE (3)
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi B  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with 3SA4_NAJKA | P60303 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA4_NAJKA   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d2bhib_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 2bhiB00 B:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee......eeeeeee........eeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------SNAKE_TOXIN          --- PROSITE (2)
                 Transcript ------------------------------------------------------------ Transcript
                  2bhi B  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BHI)

(-) Gene Ontology  (7, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (3SA3_NAJAT | P60301)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
    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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0044279    other organism membrane    A membrane of a secondary organism with which the first organism is interacting.

Chain A,B   (3SA4_NAJKA | P60303)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0044279    other organism membrane    A membrane of a secondary organism with which the first organism is interacting.

Chain A,B   (3SA3_NAJSP | P60302)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0044279    other organism membrane    A membrane of a secondary organism with which the first organism is interacting.

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 Related Entries

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

UniProtKB/Swiss-Prot
        3SA3_NAJAT | P603011h0j 1i02 1xt3 2crs 2crt
        3SA3_NAJSP | P603021h0j
        3SA4_NAJKA | P603031h0j

(-) Related Entries Specified in the PDB File

1h0j STRUCTURAL BASIS OF THE MEMBRANE-INDUCED CARDIOTOXIN A3 OLIGOMERIZATION
1i02 NMR STRUCTURE OF CTX A3 AT NEUTRAL PH (20 STRUCTURES)
1xt3 STRUCTURE BASIS OF VENOM CITRATE-DEPENDENT HEPARIN SULFATE-MEDIATED CELL SURFACE RETENTION OF COBRA CARDIOTOXIN A3
2crs CARDIOTOXIN III (NMR, 13 STRUCTURES)
2crt CARDIOTOXIN III (NMR, MINIMIZED AVERAGE STRUCTURE)