6YMV

Cryo-EM structure of yeast mitochondrial RNA polymerase partially-melted transcription initiation complex (PmIC)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	S13-like H2TH domain	8090726	3000053	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8036533	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 [auth B]	RrnaAD_C_1	e6ymvB1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: RrnaAD_C_1	ECOD (1.6)
A [auth B]	RrnaAD_N	e6ymvB2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00398	Ribosomal RNA adenine dimethylase (RrnaAD)	Ribosomal RNA adenine dimethylase	-	Domain
B [auth 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
B [auth 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
A [auth B]	Mitochondrial transcription factor 1	DNA binding binding organic cyclic compound binding nucleic acid binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity 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 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 DNA-templated transcription elongation 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 DNA-templated transcription, elongation 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 DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process methylation	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 mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space organelle envelope lumen organelle envelope mitochondrial envelope
B [auth A]	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 DNA primase activity	DNA-templated DNA replication cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process organic cyclic compound metabolic process nucleic acid biosynthetic process DNA replication DNA-templated DNA replication cellular biosynthetic process DNA replication, synthesis of primer cellular metabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process organic cyclic compound metabolic process nucleic acid biosynthetic process DNA replication organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization organelle organization mitochondrial genome maintenance cellular component organization or biogenesis mitochondrion organization mitochondrial gene expression DNA-templated transcription gene expression mitochondrial transcription 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
C [auth N]	DNA (33-MER) NON-TEMPLATE	-	-	-
D [auth T]	DNA (33-MER) template	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
A [auth B]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth B]	IPR016586	Mitochondrial transcription factor Mtf1	Family
A [auth B]	IPR023165	rRNA adenine dimethylase-like, C-terminal	Homologous Superfamily
B [auth A]	IPR029262	DNA-directed RNA polymerase, N-terminal	Domain
B [auth A]	IPR002092	DNA-directed RNA polymerase, phage-type	Family
B [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth A]	IPR024075	DNA-directed RNA polymerase, helix hairpin domain superfamily	Homologous Superfamily
B [auth A]	IPR046950	DNA-directed RNA polymerase, C-terminal domain, phage-type	Domain
B [auth A]	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily

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.