9GZM | pdb_00009gzm

Cryo-EM structure of the human mitochondrial RNA polymerase transcription initiation complex (POLRMT/TFAM/TFB2M/DNA/RNA) with a 2-mer RNA (pppGpA) and GTP poised for catalysis (pre-IC3)

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
F [auth C]	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box		Domain
F [auth C]	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
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
F [auth C]	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 nucleic acid binding transcription regulatory region nucleic acid binding mitochondrial promoter sequence-specific DNA binding chromatin binding protein binding heat shock protein binding RNA binding transcription regulator activity 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 chromatin binding protein binding heat shock protein binding RNA binding transcription regulator activity mitochondrial transcription factor activity transcription factor binding transcription coregulator binding transcription coactivator binding DNA binding, bending	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 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 DNA-templated transcription positive regulation of biological 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 biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II response to nutrient levels response to chemical response to nutrient	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex membrane-enclosed lumen intracellular membraneless organelle nucleoid mitochondrial matrix intracellular organelle lumen organelle lumen membraneless organelle mitochondrial nucleoid nucleus
E [auth R]	RNA (5'-D((GTP))-R(PA)-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
F [auth C]	IPR050342	High Mobility Group Box (HMGB)	Family
F [auth C]	IPR009071	High mobility group box domain	Domain
F [auth C]	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
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
F [auth C]	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
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.