6YLE | pdb_00006yle

Rix1-Rea1 pre-60S particle - Rix1-subcomplex, body 3 (rigid body refinement)

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	Pro_isomerase	e6yleA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
B	Ldh_1_C	e6yleB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
C, D	PF08167	rRNA processing/ribosome biogenesis (RIX1)	rRNA processing/ribosome biogenesis	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pre-rRNA-processing protein IPI3	chromatin binding binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process pre-replicative complex assembly nuclear DNA replication cell cycle DNA replication cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process pre-replicative complex assembly nuclear DNA replication cell cycle DNA replication cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cell cycle cellular component organization or biogenesis cell cycle process pre-replicative complex assembly involved in nuclear cell cycle DNA replication protein-containing complex organization pre-replicative complex assembly involved in cell cycle DNA replication protein-DNA complex assembly ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process RNA processing rRNA metabolic process organelle assembly membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly organelle organization protein-RNA complex organization ribosomal large subunit assembly ribosome assembly regulation of DNA-templated DNA replication initiation regulation of biological process regulation of cellular process DNA replication initiation biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen pre-replicative complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen pre-replicative complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear pre-replicative complex nuclear lumen endoribonuclease complex catalytic complex rixosome complex intracellular protein-containing complex endonuclease complex
C, D	Pre-rRNA-processing protein RIX1	chromatin binding binding	pre-replicative complex assembly nuclear DNA replication cell cycle DNA replication nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cell cycle cellular component organization or biogenesis cell cycle process pre-replicative complex assembly involved in nuclear cell cycle DNA replication DNA-templated DNA replication pre-replicative complex assembly nuclear DNA replication cell cycle DNA replication nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cell cycle cellular component organization or biogenesis cell cycle process pre-replicative complex assembly involved in nuclear cell cycle DNA replication DNA-templated DNA replication protein-containing complex organization primary metabolic process pre-replicative complex assembly involved in cell cycle DNA replication protein-DNA complex assembly DNA metabolic process nucleic acid metabolic process DNA replication metabolic process cellular process macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process RNA processing rRNA metabolic process organelle assembly membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly organelle organization protein-RNA complex organization ribosomal large subunit assembly ribosome assembly regulation of DNA-templated DNA replication initiation regulation of biological process regulation of cellular process DNA replication initiation biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex endoribonuclease complex catalytic complex rixosome complex intracellular protein-containing complex endonuclease complex
E [auth K]	Pre-rRNA-processing protein IPI1	chromatin binding 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 pre-replicative complex assembly nuclear DNA replication cell cycle DNA replication cellular component organization protein-DNA complex organization cellular component assembly protein-containing complex assembly cell cycle cell cycle process pre-replicative complex assembly involved in nuclear cell cycle DNA replication DNA-templated DNA replication protein-containing complex organization pre-replicative complex assembly involved in cell cycle DNA replication protein-DNA complex assembly DNA metabolic process DNA replication organelle assembly membraneless organelle assembly protein-RNA complex assembly organelle organization protein-RNA complex organization ribosomal large subunit assembly ribosome assembly regulation of DNA-templated DNA replication initiation regulation of biological process regulation of cellular process DNA replication initiation biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex endoribonuclease complex catalytic complex rixosome complex intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR045227	WD repeat-containing protein WDR18/Ipi3/RID3	Family
A, B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B	IPR001680	WD40 repeat	Repeat
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C, D	IPR012583	Pre-rRNA-processing protein RIX1, N-terminal	Domain
E [auth K]	IPR016024	Armadillo-type fold	Homologous Superfamily
E [auth K]	IPR024679	Pre-rRNA-processing protein Ipi1, N-terminal	Domain
E [auth K]	IPR011989	Armadillo-like helical	Homologous Superfamily

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.