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(-) Description

Title :  LYSENIN SPHINGOMYELIN COMPLEX
 
Authors :  L. De Colibus, A. F. P. Sonnen, K. J. Morris, C. A. Siebert, P. Abrusci, J V. Hodnik, M. Leippe, E. Volpi, G. Anderluh, R. J. C. Gilbert
Date :  10 Aug 11  (Deposition) - 19 Sep 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.12
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Toxin, Pore-Forming Toxin, Earthworm (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. De Colibus, A. F. P. Sonnen, K. J. Morris, C. A. Siebert, P. Abrusci, J. Plitzko, V. Hodnik, M. Leippe, E. Volpi, G. Anderluh, R. J. C. Gilbert
Structures Of Lysenin Reveal A Shared Evolutionary Origin For Pore-Forming Proteins And Its Mode Of Sphingomyelin Recognition.
Structure V. 20 1498 2012
PubMed-ID: 22819216  |  Reference-DOI: 10.1016/J.STR.2012.06.011

(-) Compounds

Molecule 1 - LYSENIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTETLYS1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonCOMMON BRANDLING WORM
    Organism ScientificEISENIA FETIDA
    Organism Taxid6396
    SynonymEFL1
    TissueCOELOMIC FLUID

 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
10SM1Ligand/IonTRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL]AZANIUM
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
10SM1Ligand/IonTRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL]AZANIUM
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10SM-1Ligand/IonTRIMETHYL-[2-[[(2S,3S)-2-(OCTADECANOYLAMINO)-3-OXIDANYL-BUTOXY]-OXIDANYL-PHOSPHORYL]OXYETHYL]AZANIUM
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:169 , GLY A:297BINDING SITE FOR RESIDUE SO4 A 898
2AC2SOFTWARETRP A:187 , TYR A:233BINDING SITE FOR RESIDUE SO4 A 899
3AC3SOFTWAREGLY A:23 , TYR A:24 , VAL A:25 , GLU A:27 , GLY A:30 , SER A:31 , HIS A:83 , GLU A:85BINDING SITE FOR RESIDUE 0SM A 943
4AC4SOFTWAREARG A:175 , SER B:186BINDING SITE FOR RESIDUE SO4 B 898

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:251 -Pro A:252
2Leu B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZXG)

(-) 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:293
 aligned with TXL_EISFE | O18423 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:293
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   
            TXL_EISFE     5 AAEGYEQIEVDVVAVWKEGYVYENRGSTSVDQKITITKGMKNVNSETRTVTATHSIGSTISTGDAFEIGSVEVSYSHSHEESQVSMTETEVYESKVIEHTITIPPTSKFTRWQLNADVGGADIEYMYLIDEVTPIGGTQSIPQVITSRAKIIVGRQIILGKTEIRIKHAERKEYMTVVSRKSWPAATLGHSKLFKFVLYEDWGGFRIKTLNTMYSGYEYAYSSDQGGIYFDQGTDNPKQRWAINKSLPLRHGDVVTFMNKYFTRSGLCYDDGPATNVYCLDKREDKWILEVVG 297
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.eeeeeeeeeeee......ee..eeeeee.........ee.............eeeeeeeeeeee....eeeeeeehhhhh..eeee..ee....eeeeeeeeeeee..eeeeeeeeeeeeee........eeeeeeeeee..........eeeeee.....eeeeeee..eeeeeee......eeeeee..eeeeee.........eeee.....eeee....hhhh.eee..........ee.eee.....eeeee.......eeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxg A   5 AAEGYEQIEVDVVAVWKEGYVYENRGSTSVDQKITITKGMKNVNSETRTVTATHSIGSTISTGDAFEIGSVEVSYSHSHEESQVSMTETEVYESKVIEHTITIPPTSKFTRWQLNADVGGADIEYMYLIDEVTPIGGTQSIPQVITSRAKIIVGRQIILGKTEIRIKHAERKEYMTVVSRKSWPAATLGHSKLFKFVLYEDWGGFRIKTLNTMYSGYEYAYSSDQGGIYFDQGTDNPKQRWAINKSLPLRHGDVVTFMNKYFTRSGLCYDDGPATNVYCLDKREDKWILEVVG 297
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with TXL_EISFE | O18423 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:293
                                                                                                                                                                                                                                                                                                                             297 
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295 | 
            TXL_EISFE     6 AEGYEQIEVDVVAVWKEGYVYENRGSTSVDQKITITKGMKNVNSETRTVTATHSIGSTISTGDAFEIGSVEVSYSHSHEESQVSMTETEVYESKVIEHTITIPPTSKFTRWQLNADVGGADIEYMYLIDEVTPIGGTQSIPQVITSRAKIIVGRQIILGKTEIRIKHAERKEYMTVVSRKSWPAATLGHSKLFKFVLYEDWGGFRIKTLNTMYSGYEYAYSSDQGGIYFDQGTDNPKQRWAINKSLPLRHGDVVTFMNKYFTRSGLCYDDGPATNVYCLDKREDKWILEVVG-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eeeeee...ee......eeeeeeeeeee.........ee.............eeeeeeeeeeee.....eeeeeehhhhh..eeeeeeeee...eeee.eeeeeee..eeee......eeee........eeeeeeeeee..........eeeeee.....eeeeeee..eeeeeee......eeeeee..eeeeee.........eeee.....eeee....hhhh.eee..........ee.eee.....eeeee.......eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zxg B   6 AEGYEQIEVDVVAVWKEGYVYENRGSTSVDQKITITKGMKNVNSETRTVTATHSIGSTISTGDAFEIGSVEVSYSHSHEESQVSMTETEVYESKVIEHTITIPPTSKFTRWQLNADVGGADIEYMYLIDEVTPIGGTQSIPQVITSRAKIIVGRQIILGKTEIRIKHAERKEYMTVVSRKSWPAATLGHSKLFKFVLYEDWGGFRIKTLNTMYSGYEYAYSSDQGGIYFDQGTDNPKQRWAINKSLPLRHGDVVTFMNKYFTRSGLCYDDGPATNVYCLDKREDKWILEVVGL 298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   

   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 3ZXG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZXG)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TXL_EISFE | O18423)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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: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.
    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
        TXL_EISFE | O184233zx7 3zxd 5ec5 5gaq

(-) Related Entries Specified in the PDB File

3zx7 COMPLEX OF LYSENIN WITH PHOSPHOCHOLINE
3zxd WILD-TYPE LYSENIN