6R5K | pdb_00006r5k

Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase

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)
G [auth O]	Vinculin	e6r5kO1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
F [auth N]	Vinculin	e6r5kN1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
E [auth H]	Vinculin	e6r5kH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
D [auth F]	Vinculin	e6r5kF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
B [auth D]	Vinculin	e6r5kD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
A	Vinculin	e6r5kA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth O]	PF18101	Pan3 C-terminal knob domain (Pan3_CK)	Pan3 C-terminal knob domain	This entry represents the Pan3 C-terminal knob domain.	Domain
F [auth N]	PF18101	Pan3 C-terminal knob domain (Pan3_CK)	Pan3 C-terminal knob domain	This entry represents the Pan3 C-terminal knob domain.	Domain
B [auth D], D [auth F], E [auth H]	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain
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	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth O]	PAN2-PAN3 deadenylation complex 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
F [auth N]	PAN2-PAN3 deadenylation complex 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
C [auth E]	poly(A) RNA	-	-	-
B [auth D], D [auth F], E [auth H]	Polyadenylate-binding protein, cytoplasmic and nuclear	molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding chromatin binding promoter-specific chromatin binding poly(A) binding poly-purine tract binding single-stranded RNA binding poly-pyrimidine tract binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding chromatin binding promoter-specific chromatin binding poly(A) binding poly-purine tract binding single-stranded RNA binding poly-pyrimidine tract binding poly(U) RNA binding enzyme regulator activity molecular function inhibitor activity molecular function regulator activity nuclease inhibitor activity enzyme inhibitor activity ribonuclease inhibitor activity	RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport regulation of cellular process negative regulation of biological process regulation of primary metabolic process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound 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 primary 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic 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 regulation of nuclear-transcribed mRNA poly(A) tail shortening 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 mRNA metabolic process macromolecule biosynthetic process nucleic acid 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 cellular process regulation of mRNA metabolic process mRNA 3'-end processing nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA 3'-end processing RNA processing protein biosynthetic process translational initiation protein metabolic process regulation of translational initiation regulation of protein metabolic process translation regulation of translation	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol ribosome protein-containing complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol ribosome protein-containing complex ribonucleoprotein complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	PAN2-PAN3 deadenylation complex catalytic 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth O]	IPR030844	PAN2-PAN3 deadenylation complex subunit PAN3	Family
G [auth O]	IPR000571	Zinc finger, CCCH-type	Domain
G [auth O]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
G [auth O]	IPR000719	Protein kinase domain	Domain
G [auth O]	IPR041332	Pan3, C-terminal knob domain	Domain
F [auth N]	IPR030844	PAN2-PAN3 deadenylation complex subunit PAN3	Family
F [auth N]	IPR000571	Zinc finger, CCCH-type	Domain
F [auth N]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
F [auth N]	IPR000719	Protein kinase domain	Domain
F [auth N]	IPR041332	Pan3, C-terminal knob domain	Domain
B [auth D], D [auth F], E [auth H]	IPR002004	Polyadenylate-binding protein/Hyperplastic disc protein, C-terminal	Domain
B [auth D], D [auth F], E [auth H]	IPR006515	Polyadenylate binding protein, human types 1, 2, 3, 4	Family
B [auth D], D [auth F], E [auth H]	IPR003954	RNA recognition motif domain, eukaryotic-type	Domain
B [auth D], D [auth F], E [auth H]	IPR000504	RNA recognition motif domain	Domain
B [auth D], D [auth F], E [auth H]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B [auth D], D [auth F], E [auth H]	IPR036053	PABC (PABP) domain	Homologous Superfamily
B [auth D], D [auth F], E [auth H]	IPR034364	PABP, RNA recognition motif 1	Domain
B [auth D], D [auth F], E [auth H]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B [auth D], D [auth F], E [auth H]	IPR045305	PABP, RNA recognition motif 2	Domain
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR030843	PAN2-PAN3 deadenylation complex catalytic subunit PAN2	Family
A	IPR028881	PAN2, UCH domain	Domain
A	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A	IPR048841	PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminal	Domain
A	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
A	IPR013520	Ribonuclease H-like domain	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR050785	PAN2-PAN3 complex catalytic subunit	Family
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily