4XR7 | pdb_00004xr7

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A [auth G]	UCH	e4xr7G2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
A [auth G]	RNase_T	e4xr7G1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
F [auth D]	UCH	e4xr7D1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
F [auth D]	RNase_T	e4xr7D2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
I [auth J]	UCH	e4xr7J2	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
I [auth J]	RNase_T	e4xr7J1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
L [auth A]	UCH	e4xr7A1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
L [auth A]	RNase_T	e4xr7A2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
B [auth L]	F_UNCLASSIFIED	e4xr7L3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth L]	Pkinase_Tyr	e4xr7L2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
C [auth K]	F_UNCLASSIFIED	e4xr7K3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth K]	Pkinase_Tyr	e4xr7K2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D [auth E]	F_UNCLASSIFIED	e4xr7E2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth E]	Pkinase_Tyr	e4xr7E1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e4xr7F3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth F]	Pkinase_Tyr	e4xr7F2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
G [auth H]	F_UNCLASSIFIED	e4xr7H3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth H]	Pkinase_Tyr	e4xr7H2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
H [auth I]	F_UNCLASSIFIED	e4xr7I3	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
H [auth I]	Pkinase_Tyr	e4xr7I2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
J [auth C]	F_UNCLASSIFIED	e4xr7C2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth C]	Pkinase_Tyr	e4xr7C1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
K [auth B]	F_UNCLASSIFIED	e4xr7B2	A: alpha arrays	X: Dimerization domain in caprin-1 and PAN3 (From Topology)	H: Dimerization domain in caprin-1 and PAN3 (From Topology)	T: Dimerization domain in caprin-1 and PAN3	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth B]	Pkinase_Tyr	e4xr7B1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth G]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
F [auth D]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
I [auth J]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
L [auth A]	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B [auth L]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B [auth L]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C [auth K]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C [auth K]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D [auth E]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D [auth E]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E [auth F]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
E [auth F]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
G [auth H]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
G [auth H]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
H [auth I]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
H [auth I]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
J [auth C]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
J [auth C]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
K [auth B]	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
K [auth B]	1.10.287.3700	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], F [auth D], I [auth J], L [auth A]	PF00929	Exonuclease (RNase_T)	Exonuclease	This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	PF13423	Ubiquitin carboxyl-terminal hydrolase (UCH_1)	Ubiquitin carboxyl-terminal hydrolase	This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 an ...	This is the ubiquitin carboxyl-terminal hydrolase domain found in a variety of proteins, including PAN2, one of the subunits of the poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover (consisting of PAN2 and PAN3), involved in the initial trimming of poly(A) tails [1-3].	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	PF18101	Pan3 C-terminal knob domain (Pan3_CK)	Pan3 C-terminal knob domain	This entry represents the Pan3 C-terminal knob domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], F [auth D], I [auth J], L [auth A]	PAB-dependent poly(A)-specific ribonuclease subunit PAN2	binding nucleic acid binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity binding nucleic acid binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity poly(A)-specific ribonuclease activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process DNA damage tolerance nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process DNA damage tolerance nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex PAN complex cytoplasm exoribonuclease complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex PAN complex cytoplasm exoribonuclease complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	PAB-dependent poly(A)-specific ribonuclease subunit PAN3	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups RNA binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process DNA damage tolerance nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process DNA damage tolerance nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process negative regulation of biological process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process nuclear-transcribed mRNA poly(A) tail shortening positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex PAN complex cytoplasm exoribonuclease complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex PAN complex cytoplasm exoribonuclease complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], F [auth D], I [auth J], L [auth A]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR030843	PAN2-PAN3 deadenylation complex catalytic subunit PAN2	Family
A [auth G], F [auth D], I [auth J], L [auth A]	IPR028881	PAN2, UCH domain	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR048841	PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminal	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR013520	Ribonuclease H-like domain	Domain
A [auth G], F [auth D], I [auth J], L [auth A]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR050785	PAN2-PAN3 complex catalytic subunit	Family
A [auth G], F [auth D], I [auth J], L [auth A]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A [auth G], F [auth D], I [auth J], L [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR030844	PAN2-PAN3 deadenylation complex subunit PAN3	Family
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR000571	Zinc finger, CCCH-type	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR000719	Protein kinase domain	Domain
B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], B [auth L], C [auth K], D [auth E], E [auth F], G [auth H], H [auth I], J [auth C], K [auth B]	IPR041332	Pan3, C-terminal knob domain	Domain