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Title :   CRYSTAL STRUCTURE OF LISTERIOLYSIN O

Authors :   S. Koester, O. Yildiz

Date :   30 Oct 13 (Deposition) - 23 Apr 14 (Release) - 07 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Toxin, Cholesterol Dependent Cytolysin, Membrane Perforation, Hemolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Koester, K. V. Pee, M. Hudel, M. Leustik, D. Rhinow, W. Kuehlbrandt, T. Chakraborty, O. Yildiz
Crystal Structure Of Listeriolysin O Reveals Molecular Details Of Oligomerization And Pore Formation
Nat. Commun. V. 5 3690 2014
PubMed-ID: 24751541 | Reference-DOI: 10.1038/NCOMMS4690

Molecule 1 - LISTERIOLYSIN O
	Chains	:	A
	Fragment	:	DOMAIN 1-4, RESIDUES 39-526
	Organism Scientific	:	LISTERIA MONOCYTOGENES
	Organism Taxid	:	1639

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 20)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	NA	15	Ligand/Ion	SODIUM ION
3	TAM	1	Ligand/Ion	TRIS(HYDROXYETHYL)AMINOMETHANE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:85 , PRO A:87 , GLN A:430 , LYS A:482 , TRP A:492 , HOH A:2229	BINDING SITE FOR RESIDUE ACT A1527
02	AC2	SOFTWARE	ASN A:432 , PRO A:442 , ASN A:478 , VAL A:479 , TYR A:480 , ASP A:497 , ASP A:498 , HOH A:2231	BINDING SITE FOR RESIDUE ACT A1528
03	AC3	SOFTWARE	LEU A:68 , TYR A:70 , LYS A:393 , ASP A:394 , NA A:1541	BINDING SITE FOR RESIDUE ACT A1529
04	AC4	SOFTWARE	GLU A:214 , NA A:1544 , HOH A:2160	BINDING SITE FOR RESIDUE ACT A1530
05	AC5	SOFTWARE	ASP A:207 , ASP A:208 , LYS A:220	BINDING SITE FOR RESIDUE NA A1531
06	AC6	SOFTWARE	TYR A:212 , GLN A:245 , THR A:409 , HOH A:2154 , HOH A:2167	BINDING SITE FOR RESIDUE NA A1532
07	AC7	SOFTWARE	ILE A:218 , GLY A:222 , ASN A:402 , HOH A:2079 , HOH A:2111	BINDING SITE FOR RESIDUE NA A1533
08	AC8	SOFTWARE	TYR A:440 , GLU A:446	BINDING SITE FOR RESIDUE NA A1534
09	AC9	SOFTWARE	SER A:123 , THR A:125 , ASN A:179	BINDING SITE FOR RESIDUE NA A1535
10	BC1	SOFTWARE	GLU A:209 , GLN A:216 , TYR A:406	BINDING SITE FOR RESIDUE NA A1536
11	BC2	SOFTWARE	LYS A:148 , ARG A:149 , ASN A:172	BINDING SITE FOR RESIDUE NA A1537
12	BC3	SOFTWARE	TYR A:126 , ARG A:149 , ALA A:173 , HOH A:2104	BINDING SITE FOR RESIDUE NA A1538
13	BC4	SOFTWARE	GLN A:116 , PHE A:221 , TYR A:303 , HOH A:2086	BINDING SITE FOR RESIDUE NA A1539
14	BC5	SOFTWARE	VAL A:147 , GLN A:278 , HOH A:2116	BINDING SITE FOR RESIDUE NA A1540
15	BC6	SOFTWARE	TYR A:70 , PHE A:391 , ASP A:394 , ACT A:1529	BINDING SITE FOR RESIDUE NA A1541
16	BC7	SOFTWARE	GLU A:247 , ASP A:320	BINDING SITE FOR RESIDUE NA A1542
17	BC8	SOFTWARE	ASP A:81 , GLU A:214 , SER A:215	BINDING SITE FOR RESIDUE NA A1543
18	BC9	SOFTWARE	GLU A:214 , ASN A:229 , ACT A:1530 , HOH A:2160	BINDING SITE FOR RESIDUE NA A1544
19	CC1	SOFTWARE	TYR A:348 , HOH A:2161	BINDING SITE FOR RESIDUE NA A1545
20	CC2	SOFTWARE	SER A:466 , SER A:467 , THR A:494 , VAL A:495 , ILE A:496 , ASP A:497 , ASP A:498 , TYR A:520	BINDING SITE FOR RESIDUE TAM A1546

(no "SS Bond" information available for 4CDB)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:462	-	His A:463

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TACY_LISMO_002 *	V	438	I	TACY_LISMO	---	---	A	V	438	I
2	UniProt	VAR_TACY_LISMO_003 *	K	523	S	TACY_LISMO	---	---	A	K	523	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_CYTOLYSINS	PS00481	Thiol-activated cytolysins signature.	TACY_LISMO	482-493	1	A:482-493

(no "Exon" information available for 4CDB)

Asymmetric/Biological 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
 aligned with A0A0H3GD84_L | A0A0H3GD84 from UniProtKB/TrEMBL  Length:529

    Alignment length:488
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518        
         A0A0H3GD84_L    39 MAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDN 526
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhh.........eee..........eeeee..eeeeeeeeeeeeeeee..ee.hhhhhhhh....eee.hhhhhh............eeeee..........eeee...hhhhhhhhhhhhhhhhhh.hhhhh.....eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhh.....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhhh.....hhhhhhhhhheeeeeeee........eeeeee.hhh................eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee.....eeeeeeeeeeee.....eeeeeee...........eeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------S--- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cdb A  39 MAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDN 526
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518

Chain A from PDB  Type:PROTEIN  Length:488
 aligned with TACY_LISMO | P13128 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:488
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518        
           TACY_LISMO    39 MAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDN 526
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhh.........eee..........eeeee..eeeeeeeeeeeeeeee..ee.hhhhhhhh....eee.hhhhhh............eeeee..........eeee...hhhhhhhhhhhhhhhhhh.hhhhh.....eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhh.....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhhh.....hhhhhhhhhheeeeeeee........eeeeee.hhh................eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee.....eeeeeeeeeeee.....eeeeeee...........eeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------S--- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_CYTOLY--------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cdb A  39 MAPPASPPASPKTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQHKNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDN 526
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518

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 '\|'

(no "SCOP Domain" information available for 4CDB)

(no "CATH Domain" information available for 4CDB)

(no "Pfam Domain" information available for 4CDB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A0A0H3GD84_L | A0A0H3GD84)

Chain A (TACY_LISMO | P13128)

molecular function
	GO:0015485	cholesterol binding	Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
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: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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:462 - His A:463	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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