4C0B

Structure of wild-type Clp1p-Pcf11p (454 -563) complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	cAMP-binding domain-like	8091491	3000084	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clp1 C-terminal domain-like	8091489	3002513	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Simibi-like P-loop NTPases	8091490	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8091490	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	cAMP-binding domain-like	8091491	3000084	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clp1 C-terminal domain-like	8091489	3002513	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)
A	Clp1	e4c0bA1	A: beta barrels	X: Protein CLP1 C-terminal domain (From Topology)	H: Protein CLP1 C-terminal domain (From Topology)	T: Protein CLP1 C-terminal domain	F: Clp1	ECOD (1.6)
A	CLP1_N_1	e4c0bA3	A: beta sandwiches	X: jelly-roll	H: Protein CLP1 jelly-roll domain (From Topology)	T: Protein CLP1 jelly-roll domain	F: CLP1_N_1	ECOD (1.6)
A	CLP1_P	e4c0bA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: CLP1_P	ECOD (1.6)
B	Clp1	e4c0bB1	A: beta barrels	X: Protein CLP1 C-terminal domain (From Topology)	H: Protein CLP1 C-terminal domain (From Topology)	T: Protein CLP1 C-terminal domain	F: Clp1	ECOD (1.6)
B	CLP1_N_1	e4c0bB2	A: beta sandwiches	X: jelly-roll	H: Protein CLP1 jelly-roll domain (From Topology)	T: Protein CLP1 jelly-roll domain	F: CLP1_N_1	ECOD (1.6)
B	CLP1_P	e4c0bB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: CLP1_P	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.1030	Mainly Beta	Sandwich	Jelly Rolls	Clp1, DNA binding domain	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.330	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	2.60.120.1030	Mainly Beta	Sandwich	Jelly Rolls	Clp1, DNA binding domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.330	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06807	Pre-mRNA cleavage complex II protein Clp1 (Clp1)	Pre-mRNA cleavage complex II protein Clp1	-	Family
A, B	PF16573	N-terminal beta-sandwich domain of polyadenylation factor (CLP1_N)	N-terminal beta-sandwich domain of polyadenylation factor	-	Family
A, B	PF16575	mRNA cleavage and polyadenylation factor CLP1 P-loop (CLP1_P)	mRNA cleavage and polyadenylation factor CLP1 P-loop	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or g ...	CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide [1].	Domain
C, D	PF11526	Pcf11, Clp1-interaction domain (Pfc11_Clp1_ID)	Pcf11, Clp1-interaction domain	Pcf11 is a subunit and an essential component of the cleavage and polyadenylation factor CFIA from yeast and the orthologue from human CFII which is involved in pre-mRNA 3' end processing and in transcription termination [1,3]. Pcf11-mediated termina ...	Pcf11 is a subunit and an essential component of the cleavage and polyadenylation factor CFIA from yeast and the orthologue from human CFII which is involved in pre-mRNA 3' end processing and in transcription termination [1,3]. Pcf11-mediated termination is essential for vertebrate development [2]. Pcf11 binds to Clp1, another subunit of CFIA/CFII, whose interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery [1-3]. This entry represents the Clp1-interaction region (Clp1 ID) of Pcf11 from yeast and vertebrates.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups RNA binding nucleic acid binding	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process RNA splicing tRNA metabolic process tRNA splicing, via endonucleolytic cleavage and ligation RNA splicing, via endonucleolytic cleavage and ligation tRNA processing	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle
C, D	PCF11P	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription termination of RNA polymerase II transcription, poly(A)-coupled termination of RNA polymerase II transcription, exosome-dependent	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032324	Clp1, N-terminal beta-sandwich domain	Domain
A, B	IPR032319	Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain	Domain
A, B	IPR038238	Clp1, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR038239	Clp1, N-terminal beta-sandwich domain superfamily	Homologous Superfamily
A, B	IPR045116	Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3	Family
A, B	IPR010655	Pre-mRNA cleavage complex subunit Clp1, C-terminal	Domain
A, B	IPR028606	Polyribonucleotide 5-hydroxyl-kinase Clp1	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR008942	ENTH/VHS	Homologous Superfamily
C, D	IPR047415	Pcf11, CID domain	Domain
C, D	IPR054128	Pfc11, Rna14/15 interacting domain	Domain
C, D	IPR054127	Pcf11, C-terminal domain	Domain
C, D	IPR006569	CID domain	Domain
C, D	IPR021605	Pcf11, Clp1-ID	Domain
C, D	IPR045154	Protein PCF11-like	Family

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.