2NUD

The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2nudb1	Multi-domain proteins (alpha and beta)	Antivirulence factor	Antivirulence factor	Antivirulence factor	Type III effector AvrB	(Pseudomonas savastanoi pv. glycinea ) [TaxId: 318 ],	SCOPe (2.08)
A	d2nuda1	Multi-domain proteins (alpha and beta)	Antivirulence factor	Antivirulence factor	Antivirulence factor	Type III effector AvrB	(Pseudomonas savastanoi pv. glycinea ) [TaxId: 318 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Fic-like	8036830	3001922	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fic-like	8036830	3001922	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF05394	e2nudB1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF05394	ECOD (1.6)
B	PF05394	e2nudB2	A: a+b three layers	X: a+b domain in antivirulence factor (From Topology)	H: a+b domain in antivirulence factor (From Topology)	T: a+b domain in antivirulence factor	F: PF05394	ECOD (1.6)
A	PF05394	e2nudA1	A: alpha bundles	X: Fic-like (From Topology)	H: Fic-like (From Topology)	T: Fic-like	F: PF05394	ECOD (1.6)
A	PF05394	e2nudA2	A: a+b three layers	X: a+b domain in antivirulence factor (From Topology)	H: a+b domain in antivirulence factor (From Topology)	T: a+b domain in antivirulence factor	F: PF05394	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.3290.20	Mainly Alpha	Orthogonal Bundle	Fic-like fold		CATH (4.3.0)
A	1.10.3290.20	Mainly Alpha	Orthogonal Bundle	Fic-like fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05394	Avirulence protein (AvrB_AvrC)	Avirulence protein	-	Family
C, D	PF05627	Cleavage site for pathogenic type III effector avirulence factor Avr (AvrRpt-cleavage)	Cleavage site for pathogenic type III effector avirulence factor Avr	This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein ...	This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium [1]. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Avirulence B protein	-	-	extracellular region cellular anatomical entity
C, D	RPM1-interacting protein 4	-	cellular response to stimulus regulation of plant-type hypersensitive response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus regulation of response to external stimulus negative regulation of response to biotic stimulus regulation of cellular response to stress negative regulation of biological process regulation of programmed cell death response to biotic stimulus symbiont-induced defense-related programmed cell death cellular response to stress cellular response to stimulus regulation of plant-type hypersensitive response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus regulation of response to external stimulus negative regulation of response to biotic stimulus regulation of cellular response to stress negative regulation of biological process regulation of programmed cell death response to biotic stimulus symbiont-induced defense-related programmed cell death cellular response to stress response to stress regulation of response to stress plant-type hypersensitive response innate immune response negative regulation of cellular process regulation of immune system process response to external biotic stimulus negative regulation of plant-type hypersensitive response regulation of biological process immune response response to other organism defense response negative regulation of programmed cell death negative regulation of response to stimulus regulation of innate immune response negative regulation of immune response biological regulation defense response to symbiont response to external stimulus cell death regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response cellular process programmed cell death negative regulation of innate immune response protein phosphorylation organonitrogen compound metabolic process phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process defense response to bacterium response to bacterium response to organic substance response to chemical response to molecule of bacterial origin	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol endomembrane system cell periphery plasma membrane membrane extrinsic component of plasma membrane extrinsic component of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR008798	Avirulence B/C	Family
A, B	IPR036231	Avirulence B/C superfamily	Homologous Superfamily
C, D	IPR040387	RPM1-interacting protein 4/NOI4	Family
C, D	IPR008700	RIN4, pathogenic type III effector avirulence factor Avr cleavage site	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.