6ZDT | pdb_00006zdt

Crystal structure of eukaryotic Fibrillarin with Nop56 N-terminal domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6zdta_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063662	3000118	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)
B	WD40	e6zdtB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: WD40	ECOD (v294.1)
A	WD40	e6zdtA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: WD40	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF08156	NOP5NT (NUC127) domain (NOP5NT)	NOP5NT (NUC127) domain	This N terminal domain is found in RNA-binding proteins of the NOP5 family [1].	Domain
A	PF01269	Fibrillarin (Fibrillarin)	Fibrillarin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Nucleolar protein 56	RNA binding binding snoRNA binding nucleic acid binding mRNA binding	ribonucleoprotein complex biogenesis snoRNA guided rRNA 2'-O-methylation rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribonucleoprotein complex biogenesis snoRNA guided rRNA 2'-O-methylation rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis 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 macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process rRNA 2'-O-methylation RNA methylation ribosomal small subunit biogenesis maturation of SSU-rRNA sno(s)RNA processing box C/D sno(s)RNA metabolic process box C/D sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process box C/D sno(s)RNA 3'-end processing RNA 3'-end processing	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 protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex 90S preribosome nucleoplasm box C/D methylation guide snoRNP complex sno(s)RNA-containing ribonucleoprotein complex box C/D RNP complex
A	rRNA 2'-O-methyltransferase fibrillarin	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity O-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein-glutamine N-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity N-methyltransferase activity protein methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H2A methyltransferase activity histone H2AQ104 methyltransferase activity O-methyltransferase activity RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a rRNA RNA binding binding nucleic acid binding	ribonucleoprotein complex biogenesis snoRNA guided rRNA 2'-O-methylation rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribonucleoprotein complex biogenesis snoRNA guided rRNA 2'-O-methylation rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis 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 macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process rRNA 2'-O-methylation RNA methylation regulation of cellular process regulation of primary metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase I regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase I regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process ribosomal small subunit biogenesis maturation of SSU-rRNA sno(s)RNA processing box C/D sno(s)RNA metabolic process box C/D sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process box C/D sno(s)RNA 3'-end processing RNA 3'-end processing	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 protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex 90S preribosome nucleoplasm box C/D methylation guide snoRNP complex sno(s)RNA-containing ribonucleoprotein complex box C/D RNP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR042239	Nop, C-terminal domain	Homologous Superfamily
B	IPR012974	Nucleolar protein 58/56, N-terminal	Domain
B	IPR002687	Nop domain	Domain
B	IPR012976	NOSIC	Domain
B	IPR036070	Nop domain superfamily	Homologous Superfamily
B	IPR045056	Nucleolar protein Nop56/Nop58	Family
A	IPR000692	rRNA 2'-O-methyltransferase fibrillarin-like	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR020813	Fibrillarin, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.