7Q5B

Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

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)
J [auth Y]	SCOP2B Superfamily	TATA-box binding protein-like	8036833	3000705	SCOP2B (2022-06-29)
J [auth Y]	SCOP2B Superfamily	TATA-box binding protein-like	8036831	3000705	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)
I [auth X]	PF15963	e7q5bX1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF15963	ECOD (1.6)
J [auth Y]	PF00352	e7q5bY2	A: a+b two layers	X: TBP-like	H: TATA-box binding protein-like (From Topology)	T: TATA-box binding protein-like	F: PF00352	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B], G [auth C], H [auth D]	PF17921	Integrase zinc binding domain (Integrase_H2C2)	Integrase zinc binding domain	This zinc binding domain is found in a wide variety of integrase proteins.	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	PF00665	Integrase core domain (rve)	Integrase core domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].	Domain
I [auth X]	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain
J [auth Y]	PF00352	Transcription factor TFIID (or TATA-binding protein, TBP) (TBP)	Transcription factor TFIID (or TATA-binding protein, TBP)	-	Domain
K [auth Z]	PF07741	Brf1-like TBP-binding domain (BRF1)	Brf1-like TBP-binding domain	In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1 [1]. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol I ...	In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1 [1]. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling [2]. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions [3].	Domain
K [auth Z]	PF00382	Transcription factor TFIIB repeat (TFIIB)	Transcription factor TFIIB repeat	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth R]	DNA (56-MER)	-	-	-
B [auth S]	DNA (31-MER)	-	-	-
C [auth r]	DNA (34-MER)	-	-	-
D [auth s]	DNA (9-MER)	-	-	-
E [auth A], F [auth B], G [auth C], H [auth D]	Transposon Ty3-G Gag-Pol polyprotein	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding aspartic-type peptidase activity aspartic-type endopeptidase activity endopeptidase activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA nuclease activity endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters RNA-directed DNA polymerase activity cation binding transition metal ion binding zinc ion binding metal ion binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process transposition retrotransposition DNA integration organonitrogen compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process transposition retrotransposition DNA integration organonitrogen compound metabolic process proteolysis protein metabolic process	retrotransposon nucleocapsid membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity cytoplasm
I [auth X]	Transcription factor TFIIIB component B''	transcription factor binding TFIIIC-class transcription factor complex binding protein binding binding RNA polymerase III general transcription initiation factor binding general transcription initiation factor binding RNA polymerase III general transcription initiation factor activity general transcription initiation factor activity	cellular biosynthetic process transcription preinitiation complex assembly RNA metabolic process RNA polymerase III preinitiation complex assembly RNA biosynthetic process nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process cellular component assembly organic substance biosynthetic process protein-containing complex assembly cellular biosynthetic process transcription preinitiation complex assembly RNA metabolic process RNA polymerase III preinitiation complex assembly RNA biosynthetic process nucleobase-containing compound metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process cellular component assembly organic substance biosynthetic process protein-containing complex assembly cellular component organization or biogenesis transcription initiation at RNA polymerase III promoter transcription by RNA polymerase III protein-containing complex organization cellular metabolic process primary metabolic process protein-DNA complex assembly nucleobase-containing compound biosynthetic process gene expression 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 regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of transcription by RNA polymerase III protein-containing complex remodeling protein-DNA complex remodeling DNA-templated transcription open complex formation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen RNA polymerase III transcription regulator complex protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen RNA polymerase III transcription regulator complex protein-containing complex transcription factor TFIIIB complex transcription regulator complex
J [auth Y]	TATA-box-binding protein	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding basal transcription machinery binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding TFIIA-class transcription factor complex binding RNA polymerase III transcription regulatory region sequence-specific DNA binding DNA binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding basal transcription machinery binding basal RNA polymerase II transcription machinery binding general transcription initiation factor binding RNA polymerase II general transcription initiation factor binding TFIIA-class transcription factor complex binding RNA polymerase III transcription regulatory region sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase I general transcription initiation factor binding DNA binding, bending general transcription initiation factor activity RNA polymerase II general transcription initiation factor activity core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding disordered domain specific binding protein domain specific binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process transcription preinitiation complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly transcription by RNA polymerase II protein-containing complex assembly cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter protein-containing complex organization protein-DNA complex assembly DNA-templated transcription initiation RNA polymerase II preinitiation complex assembly transcription by RNA polymerase III regulation of transcription by RNA polymerase III transcription by RNA polymerase I rRNA transcription rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I RNA polymerase I preinitiation complex assembly transcription initiation at RNA polymerase I promoter RNA polymerase III preinitiation complex assembly transcription initiation at RNA polymerase III promoter positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex RNA polymerase II transcription regulator complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex transferase complex intracellular organelle lumen intracellular organelle nucleoplasm catalytic complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex transcription factor TFIIA complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen transcription factor TFIID complex RNA polymerase III transcription regulator complex transcription factor TFIIIB complex
K [auth Z]	Transcription factor IIIB 70 kDa subunit	DNA binding binding organic cyclic compound binding nucleic acid binding RNA polymerase binding protein binding RNA polymerase core enzyme binding enzyme binding RNA polymerase III core binding RNA polymerase III type 3 promoter sequence-specific DNA binding sequence-specific DNA binding RNA polymerase III transcription regulatory region sequence-specific DNA binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding RNA polymerase binding protein binding RNA polymerase core enzyme binding enzyme binding RNA polymerase III core binding RNA polymerase III type 3 promoter sequence-specific DNA binding sequence-specific DNA binding RNA polymerase III transcription regulatory region sequence-specific DNA binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding RNA polymerase III cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding TFIIIC-class transcription factor complex binding RNA polymerase III general transcription initiation factor binding general transcription initiation factor binding RNA polymerase III general transcription initiation factor activity general transcription initiation factor activity TBP-class protein binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process transcription by RNA polymerase III regulation of RNA biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process transcription by RNA polymerase III regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase III regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process DNA-templated transcription initiation transcription preinitiation complex assembly RNA polymerase III preinitiation complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis transcription initiation at RNA polymerase III promoter protein-containing complex organization protein-DNA complex assembly protein-containing complex remodeling protein-DNA complex remodeling DNA-templated transcription open complex formation	transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen RNA polymerase III transcription regulator complex transcription factor TFIIIB complex transcription regulator complex
L [auth t], M [auth u]	DNA (19-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth C], H [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR041588	Integrase zinc-binding domain	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR001878	Zinc finger, CCHC-type	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR001584	Integrase, catalytic core	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR041577	Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR024650	Peptidase A2B, Ty3 transposon peptidase	Family
E [auth A], F [auth B], G [auth C], H [auth D]	IPR000477	Reverse transcriptase domain	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR045358	Ty3 transposon capsid-like protein	Domain
I [auth X]	IPR039467	Transcription factor TFIIIB component B'', Myb domain	Domain
I [auth X]	IPR001005	SANT/Myb domain	Domain
I [auth X]	IPR017174	Transcription factor TFIIIB component B'', fungi	Family
I [auth X]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
J [auth Y]	IPR030491	TATA-box binding protein, conserved site	Conserved Site
J [auth Y]	IPR000814	TATA-box binding protein	Family
J [auth Y]	IPR012295	TBP domain superfamily	Homologous Superfamily
J [auth Y]	IPR033710	TATA-box binding protein, eukaryotic	Family
K [auth Z]	IPR000812	Transcription factor TFIIB	Family
K [auth Z]	IPR023486	Transcription factor TFIIB, conserved site	Conserved Site
K [auth Z]	IPR011665	Brf1, TBP-binding domain	Domain
K [auth Z]	IPR013150	Transcription factor TFIIB, cyclin-like domain	Domain
K [auth Z]	IPR013137	Zinc finger, TFIIB-type	Domain
K [auth Z]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
K [auth Z]	IPR013763	Cyclin-like domain	Domain