1XL3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   COMPLEX STRUCTURE OF Y.PESTIS VIRULENCE FACTORS YOPN AND TYEA

Authors :   F. D. Schubot, M. W. Jackson, K. J. Penrose, S. Cherry, J. E. Tropea, G. V. Plano, D. S. Waugh

Date :   30 Sep 04 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Yopn, Tyea, Yersinia Pestis, Type Iii Secretion, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. D. Schubot, M. W. Jackson, K. J. Penrose, S. Cherry, J. E. Tropea, G. V. Plano, D. S. Waugh
Three-Dimensional Structure Of A Macromolecular Assembly That Regulates Type Iii Secretion In Yersinia Pestis.
J. Mol. Biol. V. 346 1147 2005
PubMed-ID: 15701523 | Reference-DOI: 10.1016/J.JMB.2004.12.036
(for further references see the PDB file header)

Molecule 1 - SECRETION CONTROL PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PDEST42
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	YOPN, LCRE
	Mutation	:	YES
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	YOP4B, LCRE

Molecule 2 - PROTEIN TYPE A
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PDEST42
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	TYEA
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 28)

No.	Name	Count	Type	Full Name
1	MLY	28	Mod. Amino Acid	N-DIMETHYL-LYSINE

Biological Unit 1 (1, 14)

No.	Name	Count	Type	Full Name
1	MLY	14	Mod. Amino Acid	N-DIMETHYL-LYSINE

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	MLY	14	Mod. Amino Acid	N-DIMETHYL-LYSINE

(no "Site" information available for 1XL3)

(no "SS Bond" information available for 1XL3)

(no "Cis Peptide Bond" information available for 1XL3)

(no "SAP(SNP)/Variant" information available for 1XL3)

(no "PROSITE Motif" information available for 1XL3)

(no "Exon" information available for 1XL3)

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:202
 aligned with YOPN_YERPE | P68640 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:206
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277      
           YOPN_YERPE    78 ARVSDVEEQVNQYLSKVPELEQKQNVSELLSLLSNSPNISLSQLKAYLEGKSEEPSEQFKMLCGLRDALKGRPELAHLSHLVEQALVSMAEEQGETIVLGARITPEAYRESQSGVNPLQPLRDTYRDAVMGYQGIYAIWSDLQKRFPNGDIDSVILFLQKALSADLQSQQSGSGREKLGIVISDLQKLKEFGSVSDQVKGFWQFFS 283
               SCOP domains d1xl3a1 A:78-283 Ou    ter membrane protein yopN (LcrE)                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....----.hhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xl3 A  78 ARVSDVEEQVNQYLSkVPE----QNVSELLSLLSNSPNISLSQLkAYLEGkSEEPSEQFkMLCGLRDALkGRPELAHLSHLVEQALVSMAEEQGETIVLGARITPEAYRESQSGVNPLQPLRDTYRDAVMGYQGIYAIWSDLQkRFPNGDIDSVILFLQkALSADLQSQQSGSGREkLGIVISDLQkLkEFGSVSDQVkGFWQFFS 283
                                    87     |  |-   |   107       117    |  127|      137       147       157       167       177       187       197       207       217   |   227       237       247      |257      |267       277      
                                          93-MLY 101                  122-MLY |      137-MLY   147-MLY                                                                   221-MLY         237-MLY          254-MLY   264-MLY     276-MLY   
                                                                            128-MLY                                                                                                                                   266-MLY

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with YOPN_YERPE | P68640 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:206
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277      
           YOPN_YERPE    78 ARVSDVEEQVNQYLSKVPELEQKQNVSELLSLLSNSPNISLSQLKAYLEGKSEEPSEQFKMLCGLRDALKGRPELAHLSHLVEQALVSMAEEQGETIVLGARITPEAYRESQSGVNPLQPLRDTYRDAVMGYQGIYAIWSDLQKRFPNGDIDSVILFLQKALSADLQSQQSGSGREKLGIVISDLQKLKEFGSVSDQVKGFWQFFS 283
               SCOP domains d1xl3b_ B: Outer membrane protein yopN (LcrE)                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) HrpJ-1xl3B01 B:78-223                                                                                                                             ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) HrpJ-1xl3B02 B:78-223                                                                                                                             ------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xl3 B  78 ARVSDVEEQVNQYLSkVPELEQKQNVSELLSLLSNSPNISLSQLkAYLEGkSEEPSEQFkMLCGLRDALkGRPELAHLSHLVEQALVSMAEEQGETIVLGARITPEAYRESQSGVNPLQPLRDTYRDAVMGYQGIYAIWSDLQkRFPNGDIDSVILFLQkALSADLQSQQSGSGREkLGIVISDLQkLkEFGSVSDQVkGFWQFFS 283
                                    87     |  97       107       117    |  127|      137       147       157       167       177       187       197       207       217   |   227       237       247      |257      |267       277      
                                          93-MLY                      122-MLY |      137-MLY   147-MLY                                                                   221-MLY         237-MLY          254-MLY   264-MLY     276-MLY   
                                                                            128-MLY                                                                                                                                   266-MLY

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with TYEA_YEREN | P69967 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    11        21        31        41        51        61        71        81        91 
           TYEA_YEREN     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
               SCOP domains d1xl3c1 C:2-92 TyeA                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1xl3 C   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
                                    11      | 21        31        41       |51        61        71        81        91 
                                           18-MLY                 41-MLY  49-MLY

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with TYEA_YERPE | P69968 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    11        21        31        41        51        61        71        81        91 
           TYEA_YERPE     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
               SCOP domains d1xl3c1 C:2-92 TyeA                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1xl3 C   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
                                    11      | 21        31        41       |51        61        71        81        91 
                                           18-MLY                 41-MLY  49-MLY

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with TYEA_YERPS | P69969 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    11        21        31        41        51        61        71        81        91 
           TYEA_YERPS     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
               SCOP domains d1xl3c1 C:2-92 TyeA                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 1xl3 C   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEEELSELD  92
                                    11      | 21        31        41       |51        61        71        81        91 
                                           18-MLY                 41-MLY  49-MLY

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with TYEA_YEREN | P69967 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
           TYEA_YEREN     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
               SCOP domains d1xl3d_ D: TyeA                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TyeA-1xl3D01 D:2-86                                                                   Pfam domains (1)
           Pfam domains (2) TyeA-1xl3D02 D:2-86                                                                   Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1xl3 D   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
                                    11      | 21        31        41       |51        61        71        81     
                                           18-MLY                 41-MLY  49-MLY

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with TYEA_YERPE | P69968 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
           TYEA_YERPE     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
               SCOP domains d1xl3d_ D: TyeA                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TyeA-1xl3D01 D:2-86                                                                   Pfam domains (1)
           Pfam domains (2) TyeA-1xl3D02 D:2-86                                                                   Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1xl3 D   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
                                    11      | 21        31        41       |51        61        71        81     
                                           18-MLY                 41-MLY  49-MLY

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with TYEA_YERPS | P69969 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
           TYEA_YERPS     2 AYDLSEFMGDIVALVDKRWAGIHDIEHLANAFSLPTPEIKVRFYQDLKRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
               SCOP domains d1xl3d_ D: TyeA                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TyeA-1xl3D01 D:2-86                                                                   Pfam domains (1)
           Pfam domains (2) TyeA-1xl3D02 D:2-86                                                                   Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1xl3 D   2 AYDLSEFMGDIVALVDkRWAGIHDIEHLANAFSLPTPEIkVRFYQDLkRMFRLFPLGVFSDEEQRQNLLQMCQNAIDMAIESEEE  86
                                    11      | 21        31        41       |51        61        71        81     
                                           18-MLY                 41-MLY  49-MLY

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Type III secretion system domain (4)

Superfamily: Type III secretion system domain (4)

Family: LcrE-like (2)

Protein domain: Outer membrane protein yopN (LcrE) (2)

Yersinia pestis [TaxId: 632] (2)

1a	d1xl3a1	A:78-283
1b	d1xl3b_	B:

Family: TyeA-like (1)

Protein domain: TyeA (1)

Yersinia pestis [TaxId: 632] (1)

2a	d1xl3c1	C:2-92
2b	d1xl3d_	D:

(no "CATH Domain" information available for 1XL3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: HrpJ] (5)

Family: HrpJ (5)

Yersinia pestis (2)

1a	HrpJ-1xl3B01	B:78-223
1b	HrpJ-1xl3B02	B:78-223

Clan: no clan defined [family: TyeA] (1)

Family: TyeA (1)

Yersinia pestis (1)

2a	TyeA-1xl3D01	D:2-86
2b	TyeA-1xl3D02	D:2-86

Asymmetric Unit(hide GO term definitions)

Chain A,B (YOPN_YERPE | P68640)

biological process
	GO:0050709	negative regulation of protein secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell.
	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.
	GO:0030254	protein secretion by the type III secretion system	The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
	GO:0046903	secretion	The controlled release of a substance by a cell or a tissue.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

Chain C,D (TYEA_YERPE | P69968)

Chain C,D (TYEA_YERPS | P69969)

Chain C,D (TYEA_YEREN | P69967)

Asymmetric Unit
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	Sites
(no "Sites" information available for 1xl3)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xl3)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1xl3
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	TYEA_YERPE \| P69968
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	TYEA_YERPS \| P69969
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	YOPN_YERPE \| P68640
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	YOPN_YERPE \| P68640
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UniProtKB/Swiss-Prot
	YOPN_YERPE \| P68640	:	1xkp

1xkp	COMPLEX OF YOPN WITH ITS HETERODIMERIC SECRETION CHAPERONE SYCN-YSCB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 28)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (8, 8)

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