4YLO | pdb_00004ylo

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA

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)
X [auth R]	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8038503	3001393	SCOP2B (2022-06-29)
O [auth L]	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8038503	3001393	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8038503	3001393	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)
V [auth P]	C1-set	e4yloP1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: C1-set	ECOD (v294.1)
M [auth J]	C1-set	e4yloJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: C1-set	ECOD (v294.1)
D	C1-set	e4yloD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: C1-set	ECOD (v294.1)
X [auth R]	SAM_KSR1_N	e4yloR1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
O [auth L]	SAM_KSR1_N	e4yloL1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
F	LAGLIDADG_1	e4yloF3	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
F	SAM_KSR1_N	e4yloF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (v294.1)
W [auth Q]	LAGLIDADG_1	e4yloQ1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
N [auth K]	LAGLIDADG_1	e4yloK1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
E	LAGLIDADG_1	e4yloE1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
U [auth O]	LAGLIDADG_1	e4yloO1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
L [auth I]	LAGLIDADG_1	e4yloI1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
C	LAGLIDADG_1	e4yloC1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
T [auth N]	LAGLIDADG_1	e4yloN1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
S [auth M]	LAGLIDADG_1	e4yloM1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
K [auth H]	LAGLIDADG_1	e4yloH2	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
J [auth G]	LAGLIDADG_1	e4yloG1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
B	LAGLIDADG_1	e4yloB2	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)
A	LAGLIDADG_1	e4yloA1	A: a/b three-layered sandwiches	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F: LAGLIDADG_1	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, M [auth J], V [auth P]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
D, M [auth J], V [auth P]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
D, M [auth J], V [auth P]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
D, M [auth J], V [auth P]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
F, O [auth L], X [auth R]	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
F, O [auth L], X [auth R]	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
F, O [auth L], X [auth R]	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
F, O [auth L], X [auth R]	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain
F, O [auth L], X [auth R]	PF04546	Sigma-70, non-essential region (Sigma70_ner)	Sigma-70, non-essential region	The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.	Domain
E, N [auth K], W [auth Q]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
C, L [auth I], U [auth O]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
C, L [auth I], U [auth O]	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
C, L [auth I], U [auth O]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
C, L [auth I], U [auth O]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
C, L [auth I], U [auth O]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C, L [auth I], U [auth O]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, M [auth J], V [auth P]	DNA-directed RNA polymerase subunit beta'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid 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 transition metal ion binding zinc ion binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to chemical response to antibiotic cellular response to stimulus cellular response to stress response to stress cellular response to cell envelope stress organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis bacterial-type flagellum organization organelle organization cellular component assembly cell projection assembly nitrate assimilation nitrogen cycle metabolic process oxoacid metabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process reactive nitrogen species metabolic process regulation of DNA-templated transcription elongation DNA-templated transcription elongation cell aggregation biofilm formation aggregation of unicellular organisms submerged biofilm formation cell motility response to heat response to abiotic stimulus response to temperature stimulus bacterial-type flagellum-dependent cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex membrane membrane-bounded organelle transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
AA [auth 9], I [auth 3], R [auth 6]	RNA (5'-D((GTP))-R(PAPGPU)-3')	-	-	-
H [auth 2], Q [auth 5], Z [auth 8]	T strand DNA (49-MER)	-	-	-
G [auth 1], P [auth 4], Y [auth 7]	NT strand DNA (49-MER)	-	-	-
F, O [auth L], X [auth R]	RNA polymerase sigma factor RpoD	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 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 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 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 transcription regulator activity DNA-binding transcription factor activity sigma factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of DNA-templated transcription initiation DNA-templated transcription initiation response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	protein-containing complex intracellular anatomical structure catalytic complex transferase complex transferase complex, transferring phosphorus-containing groups cellular anatomical structure cytosolic DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex cytoplasm cytosol intracellular protein-containing complex sigma factor antagonist complex transcription regulator complex
E, N [auth K], W [auth Q]	DNA-directed RNA polymerase subunit omega	DNA binding binding nucleic acid 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	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
C, L [auth I], U [auth O]	DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid 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 ribonucleoside binding nucleoside binding DNA binding binding nucleic acid 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity 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	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, M [auth J], V [auth P]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D, M [auth J], V [auth P]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D, M [auth J], V [auth P]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D, M [auth J], V [auth P]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D, M [auth J], V [auth P]	IPR006592	RNA polymerase, N-terminal	Domain
D, M [auth J], V [auth P]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D, M [auth J], V [auth P]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D, M [auth J], V [auth P]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D, M [auth J], V [auth P]	IPR000722	RNA polymerase, alpha subunit	Domain
D, M [auth J], V [auth P]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D, M [auth J], V [auth P]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
F, O [auth L], X [auth R]	IPR007627	RNA polymerase sigma-70 region 2	Domain
F, O [auth L], X [auth R]	IPR000943	RNA polymerase sigma-70	Domain
F, O [auth L], X [auth R]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F, O [auth L], X [auth R]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F, O [auth L], X [auth R]	IPR007630	RNA polymerase sigma-70 region 4	Domain
F, O [auth L], X [auth R]	IPR014284	RNA polymerase sigma-70-like domain	Domain
F, O [auth L], X [auth R]	IPR007624	RNA polymerase sigma-70 region 3	Domain
F, O [auth L], X [auth R]	IPR028630	RNA polymerase sigma factor RpoD	Family
F, O [auth L], X [auth R]	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
F, O [auth L], X [auth R]	IPR007127	RNA polymerase sigma factor 70, region 1.1	Domain
F, O [auth L], X [auth R]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F, O [auth L], X [auth R]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F, O [auth L], X [auth R]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F, O [auth L], X [auth R]	IPR007631	RNA polymerase sigma factor 70, non-essential domain	Domain
F, O [auth L], X [auth R]	IPR042189	Sigma-70 factor, region 1.1 superfamily	Homologous Superfamily
E, N [auth K], W [auth Q]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E, N [auth K], W [auth Q]	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E, N [auth K], W [auth Q]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
C, L [auth I], U [auth O]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C, L [auth I], U [auth O]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C, L [auth I], U [auth O]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C, L [auth I], U [auth O]	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C, L [auth I], U [auth O]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C, L [auth I], U [auth O]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C, L [auth I], U [auth O]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C, L [auth I], U [auth O]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C, L [auth I], U [auth O]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C, L [auth I], U [auth O]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C, L [auth I], U [auth O]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C, L [auth I], U [auth O]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C, L [auth I], U [auth O]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B, J [auth G], K [auth H], S [auth M], A, B, J [auth G], K [auth H], S [auth M], T [auth N]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily