4XD9 | pdb_00004xd9

Structure of Rpf2-Rrs1 complex involved in ribosome biogenesis

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)
D	SCOP2B Superfamily	Rrs1-like	8092360	3002595	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rrs1-like	8092360	3002595	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS ABD-related	8092350	3000465	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS ABD-related	8092349	3000465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS ABD-related	8092349	3000465	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS ABD-related	8092350	3000465	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)
D	RRS1	e4xd9D1	A: a+b two layers	X: Rrs1 (From Topology)	H: Rrs1 (From Topology)	T: Rrs1	F: RRS1	ECOD (1.6)
B	RRS1	e4xd9B1	A: a+b two layers	X: Rrs1 (From Topology)	H: Rrs1 (From Topology)	T: Rrs1	F: RRS1	ECOD (1.6)
C	Brix	e4xd9C1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: Brix	ECOD (1.6)
A	Brix	e4xd9A1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS (From Topology)	H: Anticodon-binding domain of Class II aaRS (From Topology)	T: Anticodon-binding domain of Class II aaRS	F: Brix	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF04939	Ribosome biogenesis regulatory protein (RRS1) (RRS1)	Ribosome biogenesis regulatory protein (RRS1)	-	Family
A, C	PF04427	Brix domain (Brix)	Brix domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)	RNA binding binding nucleic acid binding single-stranded RNA binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process maturation of SSU-rRNA endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis RNA metabolic process rRNA processing maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process maturation of SSU-rRNA endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) RNA processing rRNA metabolic process endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process metabolic process macromolecule metabolic process organelle assembly membraneless organelle assembly cellular component organization organelle organization cellular component assembly ribosome assembly	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 preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor
A, C	Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)	RNA binding binding nucleic acid binding single-stranded RNA binding rRNA binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribosomal large subunit biogenesis macromolecule biosynthetic process nucleic acid metabolic process maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process cellular process metabolic process macromolecule metabolic process maturation of LSU-rRNA organelle assembly protein-containing complex organization membraneless organelle assembly protein-RNA complex assembly cellular component organization organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly ribosome assembly	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 preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR007023	Ribosomal biogenesis regulatory protein	Family
A, C	IPR039770	Ribosome biogenesis protein Rpf2	Family
A, C	IPR007109	Brix 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.