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)
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)
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)
B	SCOP2B Superfamily	Rrs1-like	8092360	3002595	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rrs1-like	8092360	3002595	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		e4xd9A1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: MAPEG	F:	ECOD (20:10:01)
C		e4xd9C1	A: TBP-like	X: Bet v1-like	H: Bet v1-like	T: Sas-5-like_implico	F:	ECOD (20:10:01)
B		e4xd9B1	A: Type II ABC importer transmembrane domain fold	X: Type II ABC importer transmembrane domain fold	H: Type II ABC importer transmembrane domain fold	T: MitMem_reg	F:	ECOD (20:10:01)
D		e4xd9D1	A: Rossmann-like	X: Rossmann-related	H: S-adenosyl-L-methionine-dependent methyltransferases	T: Fer4, Fer4_7, Fer4_10	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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
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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR039770	Ribosome biogenesis protein Rpf2	Family
A, C	IPR007109	Brix domain	Domain
B, D	IPR007023	Ribosomal biogenesis regulatory protein	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.