3Q23

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GMPCPP and Manganese: sustrate complex II

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	EUF07994	e3q23A1	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: EUF07994	ECOD (1.6)
A	EUF07996	e3q23A3	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: EUF07996	ECOD (1.6)
A	EUF08099	e3q23A4	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: EUF08099	ECOD (1.6)
A	EUF08357	e3q23A5	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: EUF08357	ECOD (1.6)
C [auth B]	EUF07994	e3q23B1	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: EUF07994	ECOD (1.6)
C [auth B]	EUF07996	e3q23B3	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: EUF07996	ECOD (1.6)
C [auth B]	EUF08099	e3q23B4	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: EUF08099	ECOD (1.6)
C [auth B]	EUF08357	e3q23B5	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: EUF08357	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.2440	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	6.10.140.1360	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	6.10.140.1370	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	6.10.250.1860	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.30.750.220	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
A	1.20.140.110	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C [auth B]	3.30.70.2440	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C [auth B]	6.10.140.1360	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C [auth B]	6.10.140.1370	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C [auth B]	6.10.250.1860	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C [auth B]	3.30.750.220	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA		CATH (4.3.0)
C [auth B]	1.20.140.110	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF21894	Bacteriophage N4 RNA polymerase, helical domain (N4_RNAP_helical)	Bacteriophage N4 RNA polymerase, helical domain	This is a helical domain, also known as 'Fingers subdomain', found in the bacteriophage N4 virion RNA polymerase [1]. This domain possesses two essential functions of the RNAP: the N-terminal part plays a role in the nucleotide addition cycle, wherea ...	This is a helical domain, also known as 'Fingers subdomain', found in the bacteriophage N4 virion RNA polymerase [1]. This domain possesses two essential functions of the RNAP: the N-terminal part plays a role in the nucleotide addition cycle, whereas the C-terminal part is involved in promoter recognition [2]. A swing motion of the N-terminal part of the Fingers is coupled with nucleotide addition, translocation of the DNA-RNA hybrid, and downstream double-strand DNA opening.	Domain
A, C [auth B]	PF21769	Virion DNA-directed RNA polymerase domain (vRNAP_dom)	Virion DNA-directed RNA polymerase domain	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), responsible for the transcription of the early region of the double-stranded linear DNA genome of the lytic coliphage. This domain adopts a mostly alpha-helical ...	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), responsible for the transcription of the early region of the double-stranded linear DNA genome of the lytic coliphage. This domain adopts a mostly alpha-helical configuration [1-3].	Domain
A, C [auth B]	PF21867	Virion DNA-directed RNA polymerase domain (vRNAP_dom_2)	Virion DNA-directed RNA polymerase domain	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. This entr ...	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. This entry represents a region located C-terminal to the mini-vRNAP, which possesses all RNAP functions [1-3].	Domain
A, C [auth B]	PF21624	Virion DNA-directed RNA polymerase, plug insertion (vRNAP_plug)	Virion DNA-directed RNA polymerase, plug insertion	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), responsible for the transcription of the early region of the double-stranded linear DNA genome of the lytic coliphage. This entry represents a short insertion t ...	This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), responsible for the transcription of the early region of the double-stranded linear DNA genome of the lytic coliphage. This entry represents a short insertion that forms a globular module named plug, which blocks the activity of the protein [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Virion RNA polymerase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanyl nucleotide binding GTP binding guanyl ribonucleotide 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 cation binding metal ion binding	-	virion component 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
B [auth C], D	DNA (5'-D(TPGPCPCPTPCPCPCPAPGPGPCPAPTPCPCPAPAPAPAPGPAPAPGPCPGPGPAPGPCPTPTPCPTPTPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR053805	Bacteriophage N4 RNA polymerase, helical domain	Domain
A, C [auth B]	IPR049432	Virion DNA-directed RNA polymerase domain	Domain
A, C [auth B]	IPR054062	Virion DNA-directed RNA polymerase domain 2	Domain
A, C [auth B]	IPR049433	Virion DNA-directed RNA polymerase, plug insertion domain	Domain

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.