2NNW | pdb_00002nnw

Alternative conformations of Nop56/58-fibrillarin complex and implication for induced-fit assenly of box C/D RNPs

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2nnwd_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Fibrillarin homologue	Fibrillarin homologue	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)
B	d2nnwb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Fibrillarin homologue	Fibrillarin homologue	(Pyrococcus furiosus ) [TaxId: 2261 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	3000118	SCOP2B (2022-06-29)
B	SCOP2 Family	Fibrillarin homologue	8063653	4000661	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063654	3000118	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PK_Tyr_Ser-Thr	e2nnwD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
B	fn3	e2nnwB1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: fn3	ECOD (v294.1)
C	PK_Tyr_Ser-Thr	e2nnwC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: PK_Tyr_Ser-Thr	ECOD (v294.1)
C	YkuD	e2nnwC3	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)
A	ketoacyl-synt	e2nnwA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: ketoacyl-synt	ECOD (v294.1)
A	YkuD	e2nnwA2	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
A	3.30.420.220	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF01269	Fibrillarin (Fibrillarin)	Fibrillarin		Domain
A, C	PF01798	snoRNA binding domain, fibrillarin (Nop)	snoRNA binding domain, fibrillarin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase	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 RNA binding 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 RNA binding binding nucleic acid binding 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 metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing 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	-
A, C	NOP5/NOP56 related protein	RNA binding binding snoRNA binding nucleic acid binding	-	box C/D methylation guide snoRNP complex protein-containing complex sno(s)RNA-containing ribonucleoprotein complex ribonucleoprotein complex box C/D RNP complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR000692	rRNA 2'-O-methyltransferase fibrillarin-like	Family
B, D	IPR020813	Fibrillarin, conserved site	Conserved Site
B, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C	IPR042239	Nop, C-terminal domain	Homologous Superfamily
A, C	IPR036070	Nop domain superfamily	Homologous Superfamily
A, C	IPR045056	Nucleolar protein Nop56/Nop58	Family
A, C	IPR002687	Nop domain	Domain
A, C	IPR029012	Helix hairpin bin domain superfamily	Homologous Superfamily
A, C	IPR048896	Nop5/56-related, N-terminal domain	Domain
A, C	IPR012976	NOSIC	Domain
A, C	IPR047099	Nop5, N-terminal domain superfamily	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.