6H2V

Crystal structure of human METTL5-TRMT112 complex, the 18S rRNA m6A1832 methyltransferase at 2.5A resolution

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6h2va1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6h2va2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6h2vc1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6h2vc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ta1320-like	8100591	4000544	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8100592	3000118	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8100592	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)
A	Methyltransf_11_2	e6h2vA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
C	Methyltransf_11_2	e6h2vC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
B	Trm112p	e6h2vB1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)
D	Trm112p	e6h2vD1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF05175	Methyltransferase small domain (MTS)	Methyltransferase small domain	This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other methyltransferases (eg Swiss:Q53742).	Domain
B, D	PF03966	Trm112p-like protein (Trm112p)	Trm112p-like protein	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA ...	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W [1]. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast [2]. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Methyltransferase-like protein 5	RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (adenine-N6-)-methyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity rRNA (adenine-N6-)-methyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity binding organic cyclic compound binding nucleic acid binding cation binding ion binding S-adenosyl-L-methionine binding sulfur compound binding small molecule binding	regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process developmental process stem cell differentiation cellular developmental process cell differentiation ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing rRNA metabolic process nucleic acid metabolic process macromolecule methylation organic cyclic compound metabolic process RNA modification methylation macromolecule modification ncRNA metabolic process nucleic acid catabolic process RNA methylation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm cytosol fibrillar center presynapse synapse cell junction postsynapse cell projection
B, D	Multifunctional methyltransferase subunit TRM112-like protein	enzyme regulator activity enzyme activator activity molecular function activator activity methyltransferase regulator activity molecular function regulator activity tRNA methyltransferase activator activity protein heterodimerization activity protein binding binding protein dimerization activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity enzyme regulator activity enzyme activator activity molecular function activator activity methyltransferase regulator activity molecular function regulator activity tRNA methyltransferase activator activity protein heterodimerization activity protein binding binding protein dimerization activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity catalytic activity	ribonucleoprotein complex biogenesis regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis positive regulation of metabolic process ribosome biogenesis regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process ribonucleoprotein complex biogenesis regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis positive regulation of metabolic process ribosome biogenesis regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic DNA-templated transcription transcription by RNA polymerase II chromatin organization transcription initiation at RNA polymerase II promoter organic cyclic compound biosynthetic process transcription initiation-coupled chromatin remodeling positive regulation of cellular metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process chromatin remodeling positive regulation of cellular process protein-containing complex organization epigenetic regulation of gene expression nucleobase-containing compound biosynthetic process DNA-templated transcription initiation positive regulation of gene expression positive regulation of cellular biosynthetic process tRNA processing tRNA modification macromolecule methylation tRNA metabolic process RNA modification methylation macromolecule modification RNA methylation tRNA methylation organonitrogen compound metabolic process protein methylation protein alkylation peptidyl-glutamine methylation protein metabolic process protein modification process RNA (guanine-N7)-methylation rRNA methylation rRNA modification rRNA (guanine-N7)-methylation rRNA base methylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C	IPR007848	Methyltransferase small domain	Domain
B, D	IPR039127	Multifunctional methyltransferase subunit Trm112	Family
B, D	IPR005651	Trm112-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q9NRN9	hereditary spastic paraplegia osteosarcoma lung cancer plasma cell myeloma lymphoplasmacytic lymphoma psoriasis
B, D	Pharos: Q9UI30	alopecia areata diabetes mellitus leprosy ovarian cancer psoriasis vitiligo attention deficit hyperactivity disorder, inattentive type hypertensive disorder lung cancer plasma cell myeloma sclerosing cholangitis Crohn disease inflammatory bowel disease lymphoplasmacytic lymphoma primary biliary cholangitis alopecia areata diabetes mellitus leprosy ovarian cancer psoriasis vitiligo attention deficit hyperactivity disorder, inattentive type hypertensive disorder lung cancer plasma cell myeloma sclerosing cholangitis Crohn disease inflammatory bowel disease lymphoplasmacytic lymphoma primary biliary cholangitis skin basal cell carcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.