Annotations: 6ERQ

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I [auth F]	UNK_F_TYPE	e6erqF1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: UNK_F_TYPE	ECOD (1.6)
I [auth F]	RrnaAD_N	e6erqF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: RrnaAD_N	ECOD (1.6)
J	UNK_F_TYPE	e6erqJ2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: UNK_F_TYPE	ECOD (1.6)
J	RrnaAD_N	e6erqJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: RrnaAD_N	ECOD (1.6)
A [auth C]	HMG_box	e6erqC1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: HMG_box	ECOD (1.6)
D [auth G]	HMG_box	e6erqG2	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: HMG_box	ECOD (1.6)
H [auth B]	RPOL_N	e6erqB6	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N	ECOD (1.6)
H [auth B]	RNA_pol_2nd	e6erqB5	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
H [auth B]	RNA_pol_1st	e6erqB1	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
H [auth B]	KOG1038,RPOL_N	e6erqB7	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
H [auth B]	PPR_long	e6erqB3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PPR_long	ECOD (1.6)
H [auth B]	RNA_pol_3rd	e6erqB4	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)
G [auth A]	RPOL_N	e6erqA6	A: alpha arrays	X: HTH	H: HTH	T: HTH in T7 RNA polymerase	F: RPOL_N	ECOD (1.6)
G [auth A]	RNA_pol_2nd	e6erqA4	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: RNA_pol_2nd	ECOD (1.6)
G [auth A]	RNA_pol_1st	e6erqA1	A: alpha arrays	X: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	H: inserted helical bundle subdomain in T7 RNA polymerase (From Topology)	T: inserted helical bundle subdomain in T7 RNA polymerase	F: RNA_pol_1st	ECOD (1.6)
G [auth A]	KOG1038,RPOL_N	e6erqA7	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: KOG1038,RPOL_N	ECOD (1.6)
G [auth A]	PPR_long	e6erqA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PPR_long	ECOD (1.6)
G [auth A]	RNA_pol_3rd	e6erqA5	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RNA_pol_3rd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth F], J	PF00398	Ribosomal RNA adenine dimethylase (RrnaAD)	Ribosomal RNA adenine dimethylase	-	Domain
A [auth C], D [auth G]	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box	-	Domain
A [auth C], D [auth G]	PF09011	HMG-box domain (HMG_box_2)	HMG-box domain	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long ...	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].	Domain
G [auth A], H [auth B]	PF14700	DNA-directed RNA polymerase N-terminal (RPOL_N)	DNA-directed RNA polymerase N-terminal	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the ...	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex [2].	Domain
G [auth A], H [auth B]	PF00940	DNA-dependent RNA polymerase (RNA_pol)	DNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth F], J	Dimethyladenosine transferase 2, mitochondrial	RNA binding binding organic cyclic compound binding nucleic acid binding RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase 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 N-methyltransferase activity RNA binding binding organic cyclic compound binding nucleic acid binding RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase 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 N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity transcription regulator activity mitochondrial transcription factor activity	cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process transcription initiation at mitochondrial promoter DNA-templated transcription initiation ribonucleoprotein complex biogenesis rRNA methylation rRNA processing rRNA modification cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis RNA processing rRNA metabolic process macromolecule methylation RNA modification methylation macromolecule modification ncRNA metabolic process nucleic acid catabolic process RNA methylation	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle
A [auth C], D [auth G]	Transcription factor A, mitochondrial	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding transcription coactivator binding mitochondrial promoter sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding transcription coregulator binding protein binding transcription coactivator binding mitochondrial promoter sequence-specific DNA binding protein-containing complex binding chromatin binding heat shock protein binding RNA binding transcription regulator activity mitochondrial transcription factor activity	cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus regulation of cellular process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis mitochondrion organization response to nutrient levels response to chemical response to nutrient	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle protein-containing complex nucleus
B [auth D], E [auth H]	Non-Template DNA	-	-	-
C [auth E], F [auth I]	Template DNA	-	-	-
G [auth A], H [auth B]	DNA-directed RNA polymerase, mitochondrial	DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA binding 3'-5'-RNA exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity DNA primase activity RNA binding	cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process mitochondrial gene expression nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process transcription initiation at mitochondrial promoter cellular metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups RNA polymerase complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups RNA polymerase complex mitochondrial DNA-directed RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle mitochondrial nucleoid non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth F], J	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
I [auth F], J	IPR020598	Ribosomal RNA adenine methylase transferase, N-terminal	Domain
I [auth F], J	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth C], D [auth G]	IPR009071	High mobility group box domain	Domain
A [auth C], D [auth G]	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR029262	DNA-directed RNA polymerase, N-terminal	Domain
G [auth A], H [auth B]	IPR002092	DNA-directed RNA polymerase, phage-type	Family
G [auth A], H [auth B]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR046950	DNA-directed RNA polymerase, C-terminal domain, phage-type	Domain
G [auth A], H [auth B]	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth F], J	Pharos: Q9H5Q4	dermatomyositis lung cancer ovarian cancer psoriasis intellectual disability medulloblastoma pancreatic ductal adenocarcinoma lung adenocarcinoma non-small cell lung carcinoma plasma cell myeloma
A [auth C], D [auth G]	Pharos: Q00059	Alzheimer disease mitochondrial DNA depletion syndrome 15 (hepatocerebral type); secondary Parkinson disease Bowen disease of the skin Ceroid lipofuscinosis, neuronal 1, infantile plasma cell myeloma malignant mesothelioma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous neoplasm large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer ovarian cancer
G [auth A], H [auth B]	Pharos: O00411	osteosarcoma ovarian cancer

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.