9GZO | pdb_00009gzo

Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFB2M/DNA/RNA) without TFAM; and with a slipped 3-mer RNA, pppGpGpA (slipped IC3-TFAM)

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B]	PF00398	Ribosomal RNA adenine dimethylase (RrnaAD)	Ribosomal RNA adenine dimethylase		Domain
A	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
A	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
E [auth R]	RNA (5'-D((GTP))-R(PGP*A)-3')	-	-	-
D [auth B]	Dimethyladenosine transferase 2, mitochondrial	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 rRNA (adenine-N6,N6-)-dimethyltransferase activity 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 rRNA (adenine-N6,N6-)-dimethyltransferase activity RNA binding binding nucleic acid binding transcription regulator activity mitochondrial transcription factor activity	RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription initiation at mitochondrial promoter metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process 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 RNA methylation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid
C [auth T]	Template strand DNA (56-MER)	-	-	-
B [auth N]	Non-template strand DNA (56-MER)	-	-	-
A	DNA-directed RNA polymerase, mitochondrial	DNA-directed 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 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 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 hydrolase activity, acting on ester bonds nuclease activity exonuclease activity RNA binding	RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process RNA metabolic process primary metabolic process mitochondrial gene expression gene expression nucleobase-containing compound biosynthetic process mitochondrial transcription macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription initiation at mitochondrial promoter metabolic process cellular process macromolecule metabolic process mitochondrial RNA metabolic process DNA-templated DNA replication DNA metabolic process mitochondrial DNA metabolic process DNA replication mitochondrial DNA replication	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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 intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B]	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	Pharos: O00411	osteosarcoma ovarian cancer

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.