8P7B | pdb_00008p7b

CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry

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)
C [auth A]		e8p7bA01	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:	F:	ECOD (20:10:01)
A [auth B]		e8p7bB01	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:	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF08242	Methyltransferase domain (Methyltransf_12)	Methyltransferase domain	Members of this family are SAM dependent methyltransferases.	Domain
A [auth B], B [auth D]	PF00587	tRNA synthetase class II core domain (G, H, P, S and T) (tRNA-synt_2b)	tRNA synthetase class II core domain (G, H, P, S and T)	tRNA-synt_2b is a family of largely threonyl-tRNA members.	Domain
A [auth B], B [auth D]	PF02403	Seryl-tRNA synthetase N-terminal domain (Seryl_tRNA_N)	Seryl-tRNA synthetase N-terminal domain	This domain is found associated with the Pfam tRNA synthetase class II domain (Pfam:PF00587) and represents the N-terminal domain of seryl-tRNA synthetase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth R]	Serine tRNA	-	-	-
D [auth T]	Serine tRNA	-	-	-
C [auth A]	tRNA N(3)-methylcytidine methyltransferase METTL6	tRNA methyltransferase activity RNA methyltransferase activity tRNA (cytidine-3-)-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 methyltransferase activity catalytic activity protein binding binding tRNA methyltransferase activity RNA methyltransferase activity tRNA (cytidine-3-)-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 methyltransferase activity catalytic activity protein binding binding enzyme 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	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A [auth B], B [auth D]	Serine--tRNA ligase, cytoplasmic	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA binding adenyl ribonucleotide binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity selenocysteine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity serine-tRNA ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity molecular adaptor activity enzyme binding	multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression vascular endothelial growth factor production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process tRNA modification RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification tRNA processing macromolecule modification RNA processing translation protein biosynthetic process cytoplasmic translation protein metabolic process selenocysteine incorporation regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of protein metabolic process translational readthrough regulation of translation translational elongation amino acid activation tRNA aminoacylation amino acid metabolic process tRNA aminoacylation for protein translation seryl-tRNA aminoacylation regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR013217	Methyltransferase type 12	Domain
C [auth A]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C [auth A]	IPR026113	tRNA N(3)-methylcytidine methyltransferase METTL2/6/8-like	Family
A [auth B], B [auth D]	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A [auth B], B [auth D]	IPR002317	Serine-tRNA ligase, type1	Family
A [auth B], B [auth D]	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A [auth B], B [auth D]	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A [auth B], B [auth D]	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
A [auth B], B [auth D]	IPR033729	Serine-tRNA ligase catalytic core domain	Domain
A [auth B], B [auth D]	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Homologous Superfamily
A [auth B], B [auth D]	IPR015866	Serine-tRNA synthetase, type1, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: Q8TCB7	breast carcinoma breast cancer diverticulitis Malignant neoplasm of breast osteosarcoma intestinal disease ovarian cancer diabetes mellitus large cell medulloblastoma tuberculosis
A [auth B], B [auth D]	Pharos: P49591	neurodevelopmental disorder with microcephaly, ataxia, and seizures abdominal aortic aneurysm malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm epilepsy myocardial infarction pancreatic ductal adenocarcinoma peripheral arterial disease heart disease pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma

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.