1XKP

Crystal structure of the virulence factor YopN in complex with its heterodimeric chaperone SycN-YscB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xkpa1	All alpha proteins	Type III secretion system domain	Type III secretion system domain	LcrE-like	Outer membrane protein yopN (LcrE)	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)
B	d1xkpb1	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Chaperone protein SycN	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)
C	d1xkpc1	Alpha and beta proteins (a+b)	Secretion chaperone-like	Type III secretory system chaperone-like	Type III secretory system chaperone	Chaperone protein YscB	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	LcrE-like	8021383	4001357	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type III secretion system domain	8033763	3001358	SCOP2 (2022-06-29)
B	SCOP2 Family	Type III secretory system chaperone	8021385	4003372	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Type III secretory system chaperone-like	8033765	3000727	SCOP2 (2022-06-29)
C	SCOP2 Family	Type III secretory system chaperone	8021386	4003372	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Type III secretory system chaperone-like	8033766	3000727	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HrpJ	e1xkpA2	A: alpha arrays	X: Type III secretion system domain-like	H: Type III secretion system domains (From Topology)	T: Type III secretion system domains	F: HrpJ	ECOD (1.6)
A	HrpJ_like	e1xkpA1	A: alpha arrays	X: Type III secretion system domain-like	H: Type III secretion system domains (From Topology)	T: Type III secretion system domains	F: HrpJ_like	ECOD (1.6)
B	type_III_SycN	e1xkpB1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: type_III_SycN	ECOD (1.6)
C	CesT	e1xkpC1	A: a+b two layers	X: Type III secretory system chaperone-like	H: Type III secretory system chaperone (From Topology)	T: Type III secretory system chaperone	F: CesT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.10.250.670	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)
C	3.30.1460.10	Alpha Beta	2-Layer Sandwich	Yope Regulator	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF21665	Type III secretory system chaperone SycN (Type_III_SycN)	Type III secretory system chaperone SycN	Chaperone protein SycN is part of the type III secretion system and functions as a specific chaperone for YopN which may facilitate the secretion and the subsequent translocation of YopN [1].	Domain
C	PF05932	Tir chaperone protein (CesT) family (CesT)	Tir chaperone protein (CesT) family	This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion sy ...	This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment [1]. This family also contains several DspF and related sequences from several plant pathogenic bacteria. The "disease-specific" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16 kDa and 14 kDa) and acidic with predicted amphipathic alpha helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	putative membrane-bound Yop targeting protein YopN	-	negative regulation of protein transport protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of cellular process regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization negative regulation of secretion regulation of secretion by cell negative regulation of protein transport protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of cellular process regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization negative regulation of secretion regulation of secretion by cell secretion by cell cellular macromolecule localization negative regulation of cellular process negative regulation of secretion by cell negative regulation of protein localization regulation of biological process regulation of transport secretion organic substance transport biological regulation regulation of establishment of protein localization establishment of protein localization to extracellular region negative regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization regulation of secretion regulation of protein secretion negative regulation of protein secretion protein transport regulation of cellular localization macromolecule localization cellular process protein secretion by the type III secretion system transmembrane transport protein transmembrane transport	cell surface cellular anatomical entity cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane
B	Chaperone protein sycN	-	protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region localization secretion by cell protein transport cellular macromolecule localization macromolecule localization cellular process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm
C	Chaperone protein yscB	-	protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport protein secretion by the type III secretion system establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013401	Type III secretion regulator, YopN/LcrE/InvE/MxiC	Domain
A	IPR010812	Hypersensitivity response secretion-like, HrpJ	Domain
B	IPR012673	Type III secretion system chaperone SycN	Family
C	IPR010261	Tir chaperone protein (CesT) family	Family
C	IPR013353	Type III secretion system chaperone YscB	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	DMG	RESID: AA0620 PSI-MOD : N,N-dimethylglycine MOD:01983
A	MLY	Parent Component: LYS RESID: AA0620 , AA0075 PSI-MOD : N,N-dimethylglycine MOD:01983 , N6,N6-dimethyl-L-lysine MOD:00084
B	MLY	Parent Component: LYS RESID: AA0620 , AA0075 , AA0075 PSI-MOD : N,N-dimethylglycine MOD:01983 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084
C	MLY	Parent Component: LYS RESID: AA0620 , AA0075 , AA0075 , AA0075 PSI-MOD : N,N-dimethylglycine MOD:01983 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084 , N6,N6-dimethyl-L-lysine MOD:00084

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.