5FIR | pdb_00005fir

Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	PAXT-1	8105312	3002838	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	PAXT-1	8105312	3002838	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PAXT-1	8105312	3002838	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PAXT-1	8105312	3002838	SCOP2B (2022-06-29)
D	SCOP2 Family	PAXT-1	8047158	4005474	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PAXT-1	8105312	3002838	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PAXT-1	8105312	3002838	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PIN domain-like	8105313	3001041	SCOP2B (2022-06-29)
I	SCOP2 Family	XRN2-like	8051180	4007229	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	PIN domain-like	8105313	3001041	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PIN domain-like	8105313	3001041	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PIN domain-like	8105313	3001041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PIN domain-like	8105313	3001041	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PIN domain-like	8105313	3001041	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8105314	3000537	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)
L	SRP_SPB	e5firL1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: SRP_SPB	ECOD (v295.2)
J	SRP_SPB	e5firJ1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: SRP_SPB	ECOD (v295.2)
H	SRP_SPB	e5firH1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: SRP_SPB	ECOD (v295.2)
F	SRP_SPB	e5firF1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: SRP_SPB	ECOD (v295.2)
D	SRP_SPB	e5firD1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: SRP_SPB	ECOD (v295.2)
B	XTBD	e5firB1	A: alpha arrays	X: CARF (CRISPR-associated Rossmann fold) domains	H: HTH	T: winged helix domain	F: XTBD	ECOD (v295.2)
K	Cytochrom_B559,Cytochrom_B559a	e5firK2	A: alpha arrays	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Cytochrom_B559,Cytochrom_B559a	ECOD (v295.2)
K	Ribosomal_S5_C	e5firK4	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S5_C	ECOD (v295.2)
K	Ribosomal_S20p	e5firK3	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)
I	Cytochrom_B559,Cytochrom_B559a	e5firI2	A: alpha arrays	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Cytochrom_B559,Cytochrom_B559a	ECOD (v295.2)
I	Ribosomal_S5_C	e5firI4	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S5_C	ECOD (v295.2)
I	Ribosomal_S20p	e5firI3	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)
G	Cytochrom_B559,Cytochrom_B559a	e5firG2	A: alpha arrays	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Cytochrom_B559,Cytochrom_B559a	ECOD (v295.2)
G	Ribosomal_S5_C	e5firG4	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S5_C	ECOD (v295.2)
G	Ribosomal_S20p	e5firG3	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)
E	Cytochrom_B559,Cytochrom_B559a	e5firE2	A: alpha arrays	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Cytochrom_B559,Cytochrom_B559a	ECOD (v295.2)
E	Ribosomal_S5_C	e5firE4	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S5_C	ECOD (v295.2)
E	Ribosomal_S20p	e5firE3	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)
C	Cytochrom_B559,Cytochrom_B559a	e5firC2	A: alpha arrays	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Cytochrom_B559,Cytochrom_B559a	ECOD (v295.2)
C	Ribosomal_S5_C	e5firC4	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S5_C	ECOD (v295.2)
C	Ribosomal_S20p	e5firC3	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)
A	PFL-like	e5firA3	A: alpha arrays	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (v295.2)
A	PepX_N	e5firA2	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: PepX_N	ECOD (v295.2)
A	Ribosomal_S20p	e5firA1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: Ribosomal_S20p	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF11952	XRN-Two Binding Domain, XTBD (XTBD)	XRN-Two Binding Domain, XTBD	-	Family
A, C, E, G, I A, C, E, G, I, K	PF17846	Xrn1 helical domain (XRN_M)	Xrn1 helical domain	This helical domain is part of the Xrn1 catalytic core [1]. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	PAXT-1	-	catabolic process RNA metabolic process primary metabolic process miRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process miRNA metabolic process RNA catabolic process catabolic process RNA metabolic process primary metabolic process miRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process miRNA metabolic process RNA catabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA processing regulation of cellular process negative regulation of biological process positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression positive regulation of metabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process negative regulation of post-transcriptional gene silencing regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm
A, C, E, G, I A, C, E, G, I, K	5'-3' EXORIBONUCLEASE 2 HOMOLOG	hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity 5'-3' RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity cation binding transition metal ion binding hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity 5'-3' RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nucleobase-containing compound biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II termination of RNA polymerase II transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression positive regulation of metabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of gene silencing by regulatory ncRNA regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing regulation of post-transcriptional gene silencing positive regulation of gene expression negative regulation of miRNA-mediated gene silencing post-transcriptional gene silencing negative regulation of post-transcriptional gene silencing miRNA catabolic process miRNA metabolic process developmental process regulation of development, heterochronic regulation of developmental process multicellular organismal process vulval development animal organ development nematode larval development larval development regulation of vulval development multicellular organism development anatomical structure development post-embryonic development animal gross anatomical part developmental process mRNA processing RNA processing	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR057067	Partner of xrn-2 protein 1-like, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR021859	XRN2-binding (XTBD) domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR027073	5'-3' exoribonuclease	Family
A, C, E, G, I A, C, E, G, I, K	IPR041412	Xrn1, helical domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR004859	Xrn1, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR017151	5'-3' exoribonuclease type 2	Family

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.