3E3J | pdb_00003e3j

Crystal Structure of an Intermediate Complex of T7 RNAP and 8nt of 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)
A [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	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 C]		e3e3jC3	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
A [auth C]		e3e3jC6	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: EamA	F:	ECOD (20:10:01)
D [auth B]		e3e3jB1	A: HTH	X: HTH	H: winged helix domain	T: TAFII55_N	F:	ECOD (20:10:01)
D [auth B]		e3e3jB5	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: EamA	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], D [auth B]	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 [auth C], D [auth B]	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 C], D [auth B]	DNA-directed RNA polymerase	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	viral gene expression DNA-templated viral transcription viral process viral transcription 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 viral gene expression DNA-templated viral transcription viral process viral transcription 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
B [auth T], E [auth X]	DNA (28-MER)	-	-	-
C [auth N], F [auth Y]	DNA (5'-D(DTPDAPDAPDTPDAPDCPDGPDAPDCPDTPDCPDAPDCPDTPDAPDTPDAPDTPDTPDTPDCPDTPDGPDCPDCPDAPDAPDAPDCPDGPDGPDC)-3')	-	-	-
G [auth R], H [auth Z]	RNA (5'-R(GPGPGPAPGPUPAPA)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], D [auth B]	IPR029262	DNA-directed RNA polymerase, N-terminal	Domain
A [auth C], D [auth B]	IPR002092	DNA-directed RNA polymerase, phage-type	Family
A [auth C], D [auth B]	IPR024075	DNA-directed RNA polymerase, helix hairpin domain superfamily	Homologous Superfamily
A [auth C], D [auth B]	IPR046950	DNA-directed RNA polymerase, C-terminal domain, phage-type	Domain
A [auth C], D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth C], D [auth B]	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.