9IMB | pdb_00009imb

The crystal structure of human m5C methyltransferase NSUN6 bound to its S-adenosyl-L-methionine analog and a NECTIN-2 3'-UTR RNA substrate

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]		e9imbB01	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: C1-set	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], C [auth A]	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], D [auth C]	RNA (5'-R(GPCPCPCPUPCPUPUPCPAPUPCPUPCPCPAPAPAPGPAPGPGPGPC)-3')	-	-	-
A [auth B], C [auth A]	tRNA (cytosine(72)-C(5))-methyltransferase NSUN6	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (cytidine-5-)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA tRNA (cytidine) methyltransferase activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (cytidine-5-)-methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA binding nucleic acid binding	tRNA modification 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 RNA modification biosynthetic process tRNA processing macromolecule modification tRNA modification 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 RNA modification biosynthetic process tRNA processing macromolecule modification metabolic process cellular process macromolecule metabolic process RNA processing macromolecule methylation methylation RNA methylation tRNA methylation tRNA C5-cytosine methylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], C [auth A]	IPR015947	PUA-like superfamily	Homologous Superfamily
A [auth B], C [auth A]	IPR018314	RsmB/NOL1/NOP2-like, conserved site	Conserved Site
A [auth B], C [auth A]	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A [auth B], C [auth A]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth B], C [auth A]	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A [auth B], C [auth A]	IPR036974	PUA domain superfamily	Homologous Superfamily
A [auth B], C [auth A]	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], C [auth A]	Pharos: Q8TEA1	breast carcinoma Neoplasm Metastasis atypical teratoid rhabdoid tumor glioblastoma malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis bipolar disorder Brugada syndrome 4 hypertensive disorder pancreatic intraductal papillary-mucinous carcinoma breast cancer cerebrovascular disorder large cell medulloblastoma osteosarcoma breast carcinoma Neoplasm Metastasis atypical teratoid rhabdoid tumor glioblastoma malignant glioma pancreatic ductal adenocarcinoma rheumatoid arthritis bipolar disorder Brugada syndrome 4 hypertensive disorder pancreatic intraductal papillary-mucinous carcinoma breast cancer cerebrovascular disorder large cell medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.