7Q5B

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003723	molecular_function	RNA binding
A	0003824	molecular_function	catalytic activity
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0003964	molecular_function	RNA-directed DNA polymerase activity
A	0004190	molecular_function	aspartic-type endopeptidase activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0006278	biological_process	RNA-templated DNA biosynthetic process
A	0006310	biological_process	DNA recombination
A	0006508	biological_process	proteolysis
A	0008233	molecular_function	peptidase activity
A	0008270	molecular_function	zinc ion binding
A	0015074	biological_process	DNA integration
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0034061	molecular_function	DNA polymerase activity
A	0046872	molecular_function	metal ion binding
A	0071897	biological_process	DNA biosynthetic process
A	0075523	biological_process	viral translational frameshifting
B	0000166	molecular_function	nucleotide binding
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0003824	molecular_function	catalytic activity
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0003964	molecular_function	RNA-directed DNA polymerase activity
B	0004190	molecular_function	aspartic-type endopeptidase activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0006278	biological_process	RNA-templated DNA biosynthetic process
B	0006310	biological_process	DNA recombination
B	0006508	biological_process	proteolysis
B	0008233	molecular_function	peptidase activity
B	0008270	molecular_function	zinc ion binding
B	0015074	biological_process	DNA integration
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0034061	molecular_function	DNA polymerase activity
B	0046872	molecular_function	metal ion binding
B	0071897	biological_process	DNA biosynthetic process
B	0075523	biological_process	viral translational frameshifting
C	0000166	molecular_function	nucleotide binding
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003723	molecular_function	RNA binding
C	0003824	molecular_function	catalytic activity
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0003964	molecular_function	RNA-directed DNA polymerase activity
C	0004190	molecular_function	aspartic-type endopeptidase activity
C	0004518	molecular_function	nuclease activity
C	0004519	molecular_function	endonuclease activity
C	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0006278	biological_process	RNA-templated DNA biosynthetic process
C	0006310	biological_process	DNA recombination
C	0006508	biological_process	proteolysis
C	0008233	molecular_function	peptidase activity
C	0008270	molecular_function	zinc ion binding
C	0015074	biological_process	DNA integration
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0034061	molecular_function	DNA polymerase activity
C	0046872	molecular_function	metal ion binding
C	0071897	biological_process	DNA biosynthetic process
C	0075523	biological_process	viral translational frameshifting
D	0000166	molecular_function	nucleotide binding
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003723	molecular_function	RNA binding
D	0003824	molecular_function	catalytic activity
D	0003887	molecular_function	DNA-directed DNA polymerase activity
D	0003964	molecular_function	RNA-directed DNA polymerase activity
D	0004190	molecular_function	aspartic-type endopeptidase activity
D	0004518	molecular_function	nuclease activity
D	0004519	molecular_function	endonuclease activity
D	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0006278	biological_process	RNA-templated DNA biosynthetic process
D	0006310	biological_process	DNA recombination
D	0006508	biological_process	proteolysis
D	0008233	molecular_function	peptidase activity
D	0008270	molecular_function	zinc ion binding
D	0015074	biological_process	DNA integration
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0034061	molecular_function	DNA polymerase activity
D	0046872	molecular_function	metal ion binding
D	0071897	biological_process	DNA biosynthetic process
D	0075523	biological_process	viral translational frameshifting
X	0000126	cellular_component	transcription factor TFIIIB complex
X	0000995	molecular_function	RNA polymerase III general transcription initiation factor activity
X	0001112	biological_process	DNA-templated transcription open complex formation
X	0001156	molecular_function	TFIIIC-class transcription factor complex binding
X	0005515	molecular_function	protein binding
X	0005634	cellular_component	nucleus
X	0005654	cellular_component	nucleoplasm
X	0006351	biological_process	DNA-templated transcription
X	0006355	biological_process	regulation of DNA-templated transcription
X	0006359	biological_process	regulation of transcription by RNA polymerase III
X	0006383	biological_process	transcription by RNA polymerase III
X	0070898	biological_process	RNA polymerase III preinitiation complex assembly
Y	0000126	cellular_component	transcription factor TFIIIB complex
Y	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
Y	0001016	molecular_function	RNA polymerase III transcription regulatory region sequence-specific DNA binding
Y	0001092	molecular_function	TFIIA-class transcription factor complex binding
Y	0001179	molecular_function	RNA polymerase I general transcription initiation factor binding
Y	0001188	biological_process	RNA polymerase I preinitiation complex assembly
Y	0003677	molecular_function	DNA binding
Y	0003682	molecular_function	chromatin binding
Y	0005515	molecular_function	protein binding
Y	0005634	cellular_component	nucleus
Y	0005654	cellular_component	nucleoplasm
Y	0005667	cellular_component	transcription regulator complex
Y	0005669	cellular_component	transcription factor TFIID complex
Y	0005672	cellular_component	transcription factor TFIIA complex
Y	0006351	biological_process	DNA-templated transcription
Y	0006352	biological_process	DNA-templated transcription initiation
Y	0006359	biological_process	regulation of transcription by RNA polymerase III
Y	0006367	biological_process	transcription initiation at RNA polymerase II promoter
Y	0008301	molecular_function	DNA binding, bending
Y	0016251	molecular_function	RNA polymerase II general transcription initiation factor activity
Y	0032991	cellular_component	protein-containing complex
Y	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
Y	0045892	biological_process	negative regulation of DNA-templated transcription
Y	0045944	biological_process	positive regulation of transcription by RNA polymerase II
Y	0051123	biological_process	RNA polymerase II preinitiation complex assembly
Y	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
Y	0070898	biological_process	RNA polymerase III preinitiation complex assembly
Y	0097718	molecular_function	disordered domain specific binding
Y	0140297	molecular_function	DNA-binding transcription factor binding
Z	0000126	cellular_component	transcription factor TFIIIB complex
Z	0000994	molecular_function	RNA polymerase III core binding
Z	0000995	molecular_function	RNA polymerase III general transcription initiation factor activity
Z	0001006	molecular_function	RNA polymerase III type 3 promoter sequence-specific DNA binding
Z	0001112	biological_process	DNA-templated transcription open complex formation
Z	0001156	molecular_function	TFIIIC-class transcription factor complex binding
Z	0003677	molecular_function	DNA binding
Z	0005515	molecular_function	protein binding
Z	0005634	cellular_component	nucleus
Z	0005654	cellular_component	nucleoplasm
Z	0006351	biological_process	DNA-templated transcription
Z	0006352	biological_process	DNA-templated transcription initiation
Z	0006359	biological_process	regulation of transcription by RNA polymerase III
Z	0006383	biological_process	transcription by RNA polymerase III
Z	0006384	biological_process	transcription initiation at RNA polymerase III promoter
Z	0008270	molecular_function	zinc ion binding
Z	0017025	molecular_function	TBP-class protein binding
Z	0046872	molecular_function	metal ion binding
Z	0070897	biological_process	transcription preinitiation complex assembly
Z	0070898	biological_process	RNA polymerase III preinitiation complex assembly
Z	0097550	cellular_component	transcription preinitiation complex

Functional Information from PROSITE/UniProt

site_id	PS00351
Number of Residues	50
Details	TFIID Transcription factor TFIID repeat signature. YnPkrFaaVImRirePKttaLIFaSGKMvvtGAKseddsklAsrkyariI

Chain	Residue	Details
Y	TYR94-ILE143
Y	TYR185-LEU234

---

site_id	PS00782
Number of Residues	16
Details	TFIIB Transcription factor TFIIB repeat signature. GRrsqNVIASCLYVAC

Chain	Residue	Details
Z	GLY119-CYS134
Z	GLY217-CYS232

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	156
Details	Region: {"description":"Integrase-type zinc finger-like"}

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Residue

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site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

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site_id	SWS_FT_FI3
Number of Residues	4
Details	Site: {"description":"Cleavage; by Ty3 protease; partial"}

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site_id	SWS_FT_FI4
Number of Residues	165
Details	Domain: {"description":"Integrase catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU00457","evidenceCode":"ECO:0000255"}]}

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Residue

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---

site_id	SWS_FT_FI5
Number of Residues	152
Details	Repeat: {"description":"1"}

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site_id	SWS_FT_FI6
Number of Residues	156
Details	Repeat: {"description":"2"}

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---