7CRC

Cryo-EM structure of plant NLR RPP1 tetramer in complex with ATR1

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth E]	EUF07982	e7crcE3	A: alpha arrays	X: WY-domain in RXLR effectors (From Topology)	H: WY-domain in RXLR effectors (From Topology)	T: WY-domain in RXLR effectors	F: EUF07982	ECOD (1.6)
D [auth E]	EUF08035	e7crcE1	A: alpha arrays	X: ATR1 N-terminal domain (From Topology)	H: ATR1 N-terminal domain (From Topology)	T: ATR1 N-terminal domain	F: EUF08035	ECOD (1.6)
E [auth H]	EUF07982	e7crcH2	A: alpha arrays	X: WY-domain in RXLR effectors (From Topology)	H: WY-domain in RXLR effectors (From Topology)	T: WY-domain in RXLR effectors	F: EUF07982	ECOD (1.6)
E [auth H]	EUF08035	e7crcH1	A: alpha arrays	X: ATR1 N-terminal domain (From Topology)	H: ATR1 N-terminal domain (From Topology)	T: ATR1 N-terminal domain	F: EUF08035	ECOD (1.6)
F	EUF07982	e7crcF3	A: alpha arrays	X: WY-domain in RXLR effectors (From Topology)	H: WY-domain in RXLR effectors (From Topology)	T: WY-domain in RXLR effectors	F: EUF07982	ECOD (1.6)
F	EUF08035	e7crcF2	A: alpha arrays	X: ATR1 N-terminal domain (From Topology)	H: ATR1 N-terminal domain (From Topology)	T: ATR1 N-terminal domain	F: EUF08035	ECOD (1.6)
G	EUF07982	e7crcG1	A: alpha arrays	X: WY-domain in RXLR effectors (From Topology)	H: WY-domain in RXLR effectors (From Topology)	T: WY-domain in RXLR effectors	F: EUF07982	ECOD (1.6)
G	EUF08035	e7crcG3	A: alpha arrays	X: ATR1 N-terminal domain (From Topology)	H: ATR1 N-terminal domain (From Topology)	T: ATR1 N-terminal domain	F: EUF08035	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, H [auth D]	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain	-	Domain
A, B, C, H [auth D]	PF01582	TIR domain (TIR)	TIR domain	-	Family
A, B, C, H [auth D]	PF20160	C-JID domain (C-JID)	C-JID domain	C-terminal jelly roll/Ig-like domain (C-JID) was defined in cryogenic electron microscopy (cryoEM) structures of plant intracellular immune receptors containing Toll/interleukin-1 receptor (TIR, PF01582), nucleotide-binding (NB-ARC, PF00931) and leuc ...	C-terminal jelly roll/Ig-like domain (C-JID) was defined in cryogenic electron microscopy (cryoEM) structures of plant intracellular immune receptors containing Toll/interleukin-1 receptor (TIR, PF01582), nucleotide-binding (NB-ARC, PF00931) and leucine-rich repeat (LRR) domains (TIR-NLRs) [1,2]. Structurally, the C-JID core is represented by a beta-sandwich made up of 8 to 9 beta-strands. C-JID matches the so-called post-LRR or C-terminal non-LRR domain detected earlier via MEME and BLAST searches [3,7]. The domain showed a strong distribution bias towards TIR-NLRs of dicotyledonous plant species despite broader taxonomic distribution of TIR-NLR in plant groups [1-7]. Structure-function analyses of cryoEM structures suggest that C-JID domains play a role in substrate recognition, such as binding to effector proteins from pathogens, and thus are involved in the initiation of signaling by TIR-NLR receptors [1,2]. Presence of C-JID (or post-LRR) and its importance for the function of Arabidopsis TIR-NLR RPS4 that partners with RRS1 for effector recognition suggest that C-JID has additional functions [4-6].	Domain
A, B, C, H [auth D]	PF07725	Leucine Rich Repeat (LRR_3)	Leucine Rich Repeat	-	Repeat
D [auth E], E [auth H], F, G	PF22223	ATR1 N-terminal domain (ATR1_N)	ATR1 N-terminal domain	Host-adapted plant pathogens secrete numerous effectors into the host extracellular spaces or inside cells. The A. thaliana TNL receptor RPP1 confers strain-specific immunity through recognition of H.arabidopsidis effector ATR1. ATR1 consists of two ...	Host-adapted plant pathogens secrete numerous effectors into the host extracellular spaces or inside cells. The A. thaliana TNL receptor RPP1 confers strain-specific immunity through recognition of H.arabidopsidis effector ATR1. ATR1 consists of two alpha-helical domains that are involved in interactions with the receptor. The ATR1 N-terminal domain interacts with both, the C-terminal jelly roll/Ig-like domain (C-JID) and the LRRs of the RPP1 receptor [1].	Domain
D [auth E], E [auth H], F, G	PF21421	Avirulence protein ATR1, WY-domain (ATR1_WY-dom)	Avirulence protein ATR1, WY-domain	Avirulence protein ATR1 is a secreted effector that acts as an elicitor of hypersensitive response (HR) specifically on plants. It activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis NLR RPP1 [1]. This entry represents t ...	Avirulence protein ATR1 is a secreted effector that acts as an elicitor of hypersensitive response (HR) specifically on plants. It activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis NLR RPP1 [1]. This entry represents the C-terminal helical domain, referred to as the WY-domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, H [auth D]	NAD+ hydrolase (NADase)	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding ADP binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding ADP binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cellular process signal transduction cell communication defense response response to stress	-
D [auth E], E [auth H], F, G	Avirulence protein ATR1	-	biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process effector-mediated modulation of host process by symbiont modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus host intracellular organelle extracellular region host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, H [auth D]	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A, B, C, H [auth D]	IPR045344	C-JID domain	Domain
A, B, C, H [auth D]	IPR042197	Apoptotic protease-activating factors, helical domain	Homologous Superfamily
A, B, C, H [auth D]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, H [auth D]	IPR011713	Leucine-rich repeat 3	Repeat
A, B, C, H [auth D]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C, H [auth D]	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A, B, C, H [auth D]	IPR044974	Disease resistance protein, plants	Family
A, B, C, H [auth D]	IPR002182	NB-ARC	Domain
A, B, C, H [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth E], E [auth H], F, G	IPR048935	Avirulence protein ATR1, WY-domain	Domain
D [auth E], E [auth H], F, G	IPR053992	ATR1, N-terminal domain	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 R01GM157729.