3J2I | pdb_00003j2i

Structure of late pre-60S ribosomal subunits with nuclear export factor Arx1 bound at the peptide exit tunnel

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Pentein	8036230	3000640	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 [auth B]	MS_TIM-barrel,MS_N,MSG_insertion,MS_C	e3j2iB1	A: alpha bundles	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: MS_TIM-barrel,MS_N,MSG_insertion,MS_C	ECOD (develop294)
B [auth A]	Peptidase_M24	e3j2iA2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Peptidase_M24	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF01912	eIF-6 family (eIF-6)	eIF-6 family	-	Family
B [auth A]	PF00557	Metallopeptidase family M24 (Peptidase_M24)	Metallopeptidase family M24	This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Eukaryotic translation initiation factor 6	translation factor activity translation initiation factor activity ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding	maturation of 5.8S rRNA ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component organization organelle organization protein-RNA complex organization cellular component assembly assembly of large subunit precursor of preribosome protein-containing complex assembly ribosomal large subunit assembly ribosome assembly maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA cytosolic ribosome assembly establishment of organelle localization cellular localization nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear export ribosome localization	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 cytoplasm cytosol
B [auth A]	Proliferation-associated protein 2G4	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity binding nucleic acid binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding RNA binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation positive regulation of cellular process	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 membrane extracellular region extracellular exosome extracellular vesicle extracellular organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex ribonucleoprotein complex lytic vacuole intracellular vesicle cytoplasmic vesicle lumen vacuolar lumen endomembrane system cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen secretory granule primary lysosome secretory vesicle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR002769	Translation initiation factor IF6	Family
B [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR047113	Proliferation-associated protein 2G4/ARX1	Family
B [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR018349	Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site	Binding Site
B [auth A]	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
B [auth A]	IPR004545	PA2G4 family	Family
B [auth A]	IPR000994	Peptidase M24	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: Q9UQ80	vitiligo allergic rhinitis asthma Disease Exacerbation gastric cancer hereditary diffuse gastric adenocarcinoma malignant mesothelioma polycystic ovary syndrome alopecia areata attention deficit hyperactivity disorder, inattentive type gastric neoplasm large cell medulloblastoma subependymal giant cell astrocytoma anorexia nervosa cleft lip vitiligo allergic rhinitis asthma Disease Exacerbation gastric cancer hereditary diffuse gastric adenocarcinoma malignant mesothelioma polycystic ovary syndrome alopecia areata attention deficit hyperactivity disorder, inattentive type gastric neoplasm large cell medulloblastoma subependymal giant cell astrocytoma anorexia nervosa cleft lip Emery-Dreifuss muscular dystrophy Hashimoto thyroiditis lung cancer myopathy

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.