5EM2 | pdb_00005em2

Crystal structure of the Erb1-Ytm1 complex

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)
D		e5em2D1	A: Restriction endonuclease-like	X: HTH	H: winged helix domain	T: PI3_PI4_kinase	F:	ECOD (20:10:01)
B		e5em2B1	A: Restriction endonuclease-like	X: HTH	H: winged helix domain	T: PI3_PI4_kinase	F:	ECOD (20:10:01)
C		e5em2C1	A: Restriction endonuclease-like	X: HTH	H: winged helix domain	T: PI3_PI4_kinase	F:	ECOD (20:10:01)
A		e5em2A1	A: Restriction endonuclease-like	X: HTH	H: winged helix domain	T: PI3_PI4_kinase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF08154	NLE (NUC135) domain (NLE)	NLE (NUC135) domain	This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024 [1].	Domain
B, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
A, C	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Ribosome biogenesis protein YTM1	ribonucleoprotein complex binding protein-containing complex binding 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 ribosomal large subunit biogenesis maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA	preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen nuclear protein-containing complex intracellular membraneless organelle nucleolus 90S preribosome PeBoW complex membraneless organelle
A, C	Ribosome biogenesis protein ERB1	ribonucleoprotein complex binding protein-containing complex binding 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 ribosomal large subunit biogenesis maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of LSU-rRNA	preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen nuclear protein-containing complex intracellular membraneless organelle nucleolus 90S preribosome PeBoW complex membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019775	WD40 repeat, conserved site	Conserved Site
B, D	IPR012972	NLE	Domain
B, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B, D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B, D	IPR001680	WD40 repeat	Repeat
B, D	IPR028599	WD repeat WDR12/Ytm1	Family
B, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C	IPR001680	WD40 repeat	Repeat
A, C	IPR019775	WD40 repeat, conserved site	Conserved Site
A, C	IPR012953	BOP1, N-terminal domain	Domain
A, C	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, C	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C	IPR028598	WD repeat BOP1/Erb1	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.