Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7Q5B

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003723	molecular_function	RNA binding
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	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	0008270	molecular_function	zinc ion binding
A	0015074	biological_process	DNA integration
A	0046872	molecular_function	metal ion binding
A	0071897	biological_process	DNA biosynthetic process
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
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	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	0008270	molecular_function	zinc ion binding
B	0015074	biological_process	DNA integration
B	0046872	molecular_function	metal ion binding
B	0071897	biological_process	DNA biosynthetic process
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003723	molecular_function	RNA binding
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	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	0008270	molecular_function	zinc ion binding
C	0015074	biological_process	DNA integration
C	0046872	molecular_function	metal ion binding
C	0071897	biological_process	DNA biosynthetic process
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003723	molecular_function	RNA binding
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	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	0008270	molecular_function	zinc ion binding
D	0015074	biological_process	DNA integration
D	0046872	molecular_function	metal ion binding
D	0071897	biological_process	DNA biosynthetic process
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	0005634	cellular_component	nucleus
X	0005654	cellular_component	nucleoplasm
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	0006352	biological_process	DNA-templated transcription initiation
Y	0006359	biological_process	regulation of transcription by RNA polymerase III
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	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	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	32
Details	ZN_FING: TFIIB-type => ECO:0000255\|PROSITE-ProRule:PRU00469

Chain	Residue	Details
Z	MET1-GLU33
B	ARG-746-ALA-729
C	ARG-746-ALA-729
D	ARG-746-ALA-729

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00469

Chain	Residue	Details
Z	CYS4
Z	CYS7
Z	CYS25
Z	CYS28

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17287358, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
Z	SER381
B	ASP-263
B	ASP-262
B	ASP-118
B	GLU-75
B	ASP-50
B	ASP164
B	ASP225
C	ASP-325
C	ASP-263
C	ASP-262
A	ASP-263
C	ASP-118
C	GLU-75
C	ASP-50
C	ASP164
C	ASP225
D	ASP-325
D	ASP-263
D	ASP-262
D	ASP-118
D	GLU-75
A	ASP-262
D	ASP-50
D	ASP164
D	ASP225
A	ASP-118
A	GLU-75
A	ASP-50
A	ASP164
A	ASP225
B	ASP-325

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17287358

Chain	Residue	Details
Z	SER384
B	TYR0
C	GLY-804
C	HIS-778
C	HIS-702
C	SER-476
C	TYR0
D	GLY-804
D	HIS-778
D	HIS-702
D	SER-476
A	HIS-778
D	TYR0
A	HIS-702
A	SER-476
A	TYR0
B	GLY-804
B	HIS-778
B	HIS-702
B	SER-476

site_id	SWS_FT_FI5
Number of Residues	4
Details	SITE: Cleavage; by Ty3 protease => ECO:0000255

Chain	Residue	Details
A	ASN-569
B	ASN-569
C	ASN-569
D	ASN-569

site_id	SWS_FT_FI6
Number of Residues	4
Details	SITE: Cleavage; by Ty3 protease; partial

Chain	Residue	Details
A	SER26
B	SER26
C	SER26
D	SER26

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N-acetylserine => ECO:0000269\|PubMed:15956549

Chain	Residue	Details
A	SER-1009
B	SER-1009
C	SER-1009
D	SER-1009

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)