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(-) Description

Title :  STRUCTURAL BASIS OF THE MEMBRANE-INDUCED CARDIOTOXIN A3 OLIGOMERIZATION
 
Authors :  F. Forouhar, W. -N. Huang, J. -H. Liu, K. -Y. Chien, W. -G. Wu, C. -D. Hsiao
Date :  20 Jun 02  (Deposition) - 19 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cardiotoxin, Sodium Dodecyl Sulfate, Venom, Cytotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, W. -N. Huang, J. -H. Liu, K. -Y. Chien, W. -G. Wu, C. -D. Hsiao
Structural Basis Of Membrane-Induced Cardiotoxin A3 Oligomerization
J. Biol. Chem. V. 278 21980 2003
PubMed-ID: 12660250  |  Reference-DOI: 10.1074/JBC.M208650200

(-) Compounds

Molecule 1 - CARDIOTOXIN-3
    Chains: A, B, C
    Organ: VENOM GLAND
    Organism Common: CHINESE COBRA
    Organism Scientific: NAJA ATRA
    Organism Taxid: 8656
    Other Details: SODIUM DODECYL SULFATE
    Synonym: CARDIOTOXIN ANALOG III, CTX III, CARDIOTOXIN C-10 CYTOTOXIN IV, CTX-3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1SDS10Ligand/IonDODECYL SULFATE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SDS3Ligand/IonDODECYL SULFATE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SDS5Ligand/IonDODECYL SULFATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SDS2Ligand/IonDODECYL SULFATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:30 , LYS A:31 , HOH A:2047 , HOH A:2078 , HOH A:2079 , HOH A:2080 , SER C:46BINDING SITE FOR RESIDUE SDS A1061
02AC2SOFTWARELEU A:6 , PRO A:8 , PRO A:33 , ARG A:36BINDING SITE FOR RESIDUE SDS A1062
03AC3SOFTWARELYS A:5 , LYS A:12 , HOH A:2083 , HOH A:2084 , LYS B:31BINDING SITE FOR RESIDUE SDS A1063
04AC4SOFTWARELYS B:5 , LEU B:6 , VAL B:7 , PHE B:10BINDING SITE FOR RESIDUE SDS B1061
05AC5SOFTWARELYS A:44 , SER A:46 , LEU A:47 , LEU B:6 , LYS B:35 , HOH B:2008 , HOH B:2060 , HOH B:2086BINDING SITE FOR RESIDUE SDS B1062
06AC6SOFTWARETHR B:29 , PRO B:30 , LYS B:31 , VAL C:27 , ALA C:28 , HOH C:2044BINDING SITE FOR RESIDUE SDS B1063
07AC7SOFTWAREVAL B:32 , PRO B:33 , ARG B:36 , HOH B:2046BINDING SITE FOR RESIDUE SDS B1064
08AC8SOFTWARELEU A:6 , HOH A:2052 , HOH A:2053 , LYS B:44 , SER B:45 , SER B:46 , LEU B:47 , LYS B:50BINDING SITE FOR RESIDUE SDS B1065
09AC9SOFTWARELYS A:44 , LYS C:31 , HOH C:2085BINDING SITE FOR RESIDUE SDS C1061
10BC1SOFTWARETHR A:13 , THR C:29 , PRO C:30 , LYS C:31 , VAL C:32 , VAL C:34BINDING SITE FOR RESIDUE SDS C1062

(-) SS Bonds  (12, 12)

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
9C:3 -C:21
10C:14 -C:38
11C:42 -C:53
12C:54 -C:59

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H0J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H0J)

(-) PROSITE Motifs  (1, 3)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1H0J)

(-) 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 d1h0ja_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jA00 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
                  1h0j 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 d1h0ja_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jA00 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
                  1h0j 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 d1h0ja_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jA00 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
                  1h0j 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 d1h0jb_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jB00 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
                  1h0j 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 d1h0jb_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jB00 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
                  1h0j 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 d1h0jb_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jB00 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
                  1h0j B  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60


Chain C 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 d1h0jc_ C: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jC00 C: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
                  1h0j C  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60


Chain C 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 d1h0jc_ C: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jC00 C: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
                  1h0j C  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60


Chain C 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 d1h0jc_ C: Cardiotoxin III                                   SCOP domains
               CATH domains 1h0jC00 C: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
                  1h0j C  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, 3)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H0J)

(-) Gene Ontology  (7, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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,C   (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,C   (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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  1h0j
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        3SA3_NAJAT | P60301: 1i02 1xt3 2bhi 2crs 2crt
        3SA3_NAJSP | P60302: 2bhi
        3SA4_NAJKA | P60303: 2bhi

(-) Related Entries Specified in the PDB File

2crs CARDIOTOXIN III (NMR, 13 STRUCTURES)
2crt CARDIOTOXIN III (NMR, MINIMIZED AVERAGE STRUCTURE)