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(-) Description

Title :  CRYSTAL STRUCTURE OF PNEUMOLYSIN D168A MUTANT.
 
Authors :  K. Van Pee, O. Yildiz
Date :  10 Sep 15  (Deposition) - 05 Oct 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Toxin, Cholesterol Dependent Cytolysin, Pore Forming Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Van Pee, A. Neuhaus, E. D'Imprima, D. J. Mills, W. Kuhlbrandt, O. Yildiz
Cryoem Structures Of Membrane Pore And Prepore Complex Reveal Cytolytic Mechanism Of Pneumolysin.
Elife V. 6 2017
PubMed-ID: 28323617  |  Reference-DOI: 10.7554/ELIFE.23644

(-) Compounds

Molecule 1 - PNEUMOLYSIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: THIOL-ACTIVATED CYTOLYSIN, CHOLESTEROL DEPENDENT CYTOLYSIN

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5AOE)

(-) Sites  (0, 0)

(no "Site" information available for 5AOE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AOE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:406 -His A:407
2Ala B:406 -His B:407

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AOE)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_CYTOLYSINSPS00481 Thiol-activated cytolysins signature.TACY_STRP2426-437
 		  2A:426-437
B:426-437
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_CYTOLYSINSPS00481 Thiol-activated cytolysins signature.TACY_STRP2426-437
 		  1A:426-437
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_CYTOLYSINSPS00481 Thiol-activated cytolysins signature.TACY_STRP2426-437
 		  1-
B:426-437

(-) Exons   (0, 0)

(no "Exon" information available for 5AOE)

(-) 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:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh...hhhhhheee..........eeee...eeeeeeeeeeeeeeee.eee.............eee.hhhhhh............eeeeee.........eeee...hhhhhhhhhhhhhhhhhhhh........eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhh.....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhh.........hhhhhhheeeeeeee.......eeeeee...hhhhhhhhh.........eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee....eeeeeeeeeeeee.....eeeeeee.......ee..eeeeeee...eeeeeeeeeee.......eeeeeee.......eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aoe A -16 AHHHHHHSSGLVPRGSHMANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDETLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQLKVKFGSAFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSVAYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRNGQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND 471
                                    -7         3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        


Chain B from PDB  Type:PROTEIN  Length:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh...hhhhhheee..........eeee...eeeeeeeeeeeeeeee.eee.............eee.hhhhhh............eeeeee....hhhhheeee...hhhhhhhhhhhhhhhhhhhh........eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhh.....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhhh.......hhhhhhh.eeeeeeee.......ee.......hhhhhhhhh.........eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee.....eeeeeeeeeeee.....eeeeeee...........eeeeeee...eeeeeeeeeee.......eeeeeeeeee....eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aoe B -16 AHHHHHHSSGLVPRGSHMANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDETLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQLKVKFGSAFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSVAYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRNGQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND 471
                                    -7         3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463
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  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 5AOE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AOE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AOE)

(-) Gene Ontology  (10, 10)

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  Cis Peptide Bonds
    Ala A:406 - His A:407   [ RasMol ]  
    Ala B:406 - His B:407   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        TACY_STRP2 | Q04IN8: 4zgh 5aod 5aof 5cr6 5cr8 5ly6

(-) Related Entries Specified in the PDB File

5aod CRYSTAL STRUCTURE OF WILD TYPE PNEUMOLYSIN.
5aof CRYSTAL STRUCTURE OF PNEUMOLYSIN DELETION MUTANT DELTA146_147.