1L2W - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE YERSINIA VIRULENCE EFFECTOR YOPE CHAPERONE-BINDING DOMAIN IN COMPLEX WITH ITS SECRETION CHAPERONE, SYCE

Authors :   S. C. Birtalan, R. M. Phillips, P. Ghosh

Date :   25 Feb 02 (Deposition) - 12 Jun 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,I  (1x)
Biol. Unit 2: C,D,J  (1x)
Biol. Unit 3: E,F,K  (1x)
Biol. Unit 4: G,H,L  (1x)
Biol. Unit 5: C,D,G,H,J,L  (1x)
Biol. Unit 6: A (1x),B (1x),E (1x),F (1x),I (1x),K (1x)

Keywords :   Chaperone And Virulence Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Birtalan, R. M. Phillips, P. Ghosh
Three-Dimensional Secretion Signals In Chaperone-Effector Complexes Of Bacterial Pathogens.
Mol. Cell V. 9 971 2002
PubMed-ID: 12049734 | Reference-DOI: 10.1016/S1097-2765(02)00529-4
(for further references see the PDB file header)

Molecule 1 - YOPE REGULATOR
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SYCE
	Organism Scientific	:	YERSINIA PSEUDOTUBERCULOSIS
	Organism Taxid	:	633
	Synonym	:	YOPE CHAPERONE SYCE

Molecule 2 - OUTER MEMBRANE VIRULENCE PROTEIN YOPE
	Chains	:	I, J, K, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CHAPERONE-BINDING DOMAIN
	Gene	:	YOPE
	Organism Scientific	:	YERSINIA PSEUDOTUBERCULOSIS
	Organism Taxid	:	633

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B							I
Biological Unit 2 (1x)	:			C	D						J
Biological Unit 3 (1x)	:					E	F					K
Biological Unit 4 (1x)	:							G	H				L
Biological Unit 5 (1x)	:			C	D			G	H		J		L
Biological Unit 6 (1x)	:	A (1x)	B (1x)			E (1x)	F (1x)			I (1x)		K (1x)

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1L2W)

(no "Site" information available for 1L2W)

(no "SS Bond" information available for 1L2W)

Asymmetric Unit

No.	Residues
1	His A:41	-	Pro A:42
2	His B:41	-	Pro B:42
3	His C:41	-	Pro C:42
4	His D:41	-	Pro D:42
5	His E:41	-	Pro E:42
6	His F:41	-	Pro F:42
7	His G:41	-	Pro G:42
8	His H:41	-	Pro H:42

(no "SAP(SNP)/Variant" information available for 1L2W)

(no "PROSITE Motif" information available for 1L2W)

(no "Exon" information available for 1L2W)

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:122
                                                                                                                                                          
               SCOP domains d1l2wa_ A: YopE chaperone SycE                                                                                             SCOP domains
               CATH domains 1l2wA00 A:0-121  [code=3.30.1460.10, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........eeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w A   0 MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSS 121
                                     9        19        29        39        49        59        69        79        89        99       109       119

Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d1l2wb_ B: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1l2wB00 B:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w B   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d1l2wc_ C: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1l2wC00 C:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w C   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d1l2wd_ D: YopE chaperone SycE                                                                                            SCOP domains
               CATH domains 1l2wD00 D:0-120  [code=3.30.1460.10, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w D   0 MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTS 120
                                     9        19        29        39        49        59        69        79        89        99       109       119

Chain E from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d1l2we_ E: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1l2wE00 E:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w E   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain F from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d1l2wf_ F: YopE chaperone SycE                                                                                          SCOP domains
               CATH domains 1l2wF00 F:0-118  [code=3.30.1460.10, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........eeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w F   0 MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                     9        19        29        39        49        59        69        79        89        99       109

Chain G from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains d1l2wg_ G: YopE chaperone SycE                                                                                          SCOP domains
               CATH domains 1l2wG00 G:0-118  [code=3.30.1460.10, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........eeeee..eeeeeee....eeeeee........hhhhhhhh..........eeeee....eeeeeeeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w G   0 MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                     9        19        29        39        49        59        69        79        89        99       109

Chain H from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains d1l2wh_ H: YopE chaperone SycE                                                                                        SCOP domains
               CATH domains 1l2wH00 H:2-118  [code=3.30.1460.10, no name defined]                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeeee..eeeeeee....eeeeee........hhhhhhhhhh........eeeee....eeeeeeeee.hhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1l2w H   2 YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain I from PDB  Type:PROTEIN  Length:57
 aligned with YOPE_YERPS | P08008 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:57
                                    31        41        51        61        71       
           YOPE_YERPS    22 SVGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
               SCOP domains d1l2wi_ I: YopE chaperone SycE                            SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeee..hhhhhhhhh..............eee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 1l2w I  22 SVGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
                                    31        41        51        61        71

Chain J from PDB  Type:PROTEIN  Length:56
 aligned with YOPE_YERPS | P08008 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:56
                                    32        42        52        62        72      
           YOPE_YERPS    23 VGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
               SCOP domains d1l2wj_ J: YopE chaperone SycE                           SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeee..hhhhhhhhh..............eee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1l2w J  23 VGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
                                    32        42        52        62        72

Chain K from PDB  Type:PROTEIN  Length:55
 aligned with YOPE_YERPS | P08008 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:55
                                    33        43        53        63        73     
           YOPE_YERPS    24 GEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
               SCOP domains d1l2wk_ K: YopE chaperone SycE                          SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeeee..hhhhhhhhh..............eee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 1l2w K  24 GEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
                                    33        43        53        63        73

Chain L from PDB  Type:PROTEIN  Length:55
 aligned with YOPE_YERPS | P08008 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:55
                                    33        43        53        63        73     
           YOPE_YERPS    24 GEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
               SCOP domains d1l2wl_ L: YopE chaperone SycE                          SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
           Pfam domains (1) YopE_N-1l2wL01 L:24-78                                  Pfam domains (1)
           Pfam domains (2) YopE_N-1l2wL02 L:24-78                                  Pfam domains (2)
           Pfam domains (3) YopE_N-1l2wL03 L:24-78                                  Pfam domains (3)
           Pfam domains (4) YopE_N-1l2wL04 L:24-78                                  Pfam domains (4)
         Sec.struct. author .......eeee..hhhhhhhhh..............eee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 1l2w L  24 GEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF  78
                                    33        43        53        63        73

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: Alpha and beta proteins (a+b) (23004)

Fold: Secretion chaperone-like (60)

Superfamily: Type III secretory system chaperone-like (19)

Family: Type III secretory system chaperone (14)

Protein domain: YopE chaperone SycE (4)

Yersinia pestis [TaxId: 632] (3)

1a	d1l2wa_	A:
1b	d1l2wg_	G:
1c	d1l2wh_	H:
1d	d1l2wi_	I:
1e	d1l2wj_	J:
1f	d1l2wk_	K:
1g	d1l2wl_	L:
1h	d1l2wb_	B:
1i	d1l2wc_	C:
1j	d1l2wd_	D:
1k	d1l2we_	E:
1l	d1l2wf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Yope Regulator; Chain: A, (26)

Homologous Superfamily: [code=3.30.1460.10, no name defined] (12)

Yersinia pseudotuberculosis. Organism_taxid: 633. (2)

1a	1l2wA00	A:0-121
1b	1l2wD00	D:0-120
1c	1l2wF00	F:0-118
1d	1l2wG00	G:0-118
1e	1l2wB00	B:2-118
1f	1l2wC00	C:2-118
1g	1l2wE00	E:2-118
1h	1l2wH00	H:2-118

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: YopE_N (1)

Yersinia pseudotuberculosis (1)

1a	YopE_N-1l2wL01	L:24-78
1b	YopE_N-1l2wL02	L:24-78
1c	YopE_N-1l2wL03	L:24-78
1d	YopE_N-1l2wL04	L:24-78

Asymmetric Unit(hide GO term definitions)

Chain I,J,K,L (YOPE_YERPS | P08008)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
biological process
	GO:0050765	negative regulation of phagocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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(no "Sites" information available for 1l2w)

	Cis Peptide Bonds
		His A:41 - Pro A:42	[ RasMol ]
		His B:41 - Pro B:42	[ RasMol ]
		His C:41 - Pro C:42	[ RasMol ]
		His D:41 - Pro D:42	[ RasMol ]
		His E:41 - Pro E:42	[ RasMol ]
		His F:41 - Pro F:42	[ RasMol ]
		His G:41 - Pro G:42	[ RasMol ]
		His H:41 - Pro H:42	[ RasMol ]

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	1l2w
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (8, 8)

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