9G2C

Yeast RNA polymerase I elongation complex stalled by an apurinic site, open state

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005730	cellular_component	nucleolus
A	0005736	cellular_component	RNA polymerase I complex
A	0006352	biological_process	DNA-templated transcription initiation
A	0006360	biological_process	transcription by RNA polymerase I
A	0006361	biological_process	transcription initiation at RNA polymerase I promoter
A	0006362	biological_process	transcription elongation by RNA polymerase I
A	0006363	biological_process	termination of RNA polymerase I transcription
A	0008270	molecular_function	zinc ion binding
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042254	biological_process	ribosome biogenesis
A	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
A	0046872	molecular_function	metal ion binding
A	1990841	molecular_function	promoter-specific chromatin binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005730	cellular_component	nucleolus
B	0005736	cellular_component	RNA polymerase I complex
B	0006352	biological_process	DNA-templated transcription initiation
B	0006360	biological_process	transcription by RNA polymerase I
B	0006361	biological_process	transcription initiation at RNA polymerase I promoter
B	0006362	biological_process	transcription elongation by RNA polymerase I
B	0006363	biological_process	termination of RNA polymerase I transcription
B	0008270	molecular_function	zinc ion binding
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0031981	cellular_component	nuclear lumen
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0042254	biological_process	ribosome biogenesis
B	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
B	0046872	molecular_function	metal ion binding
B	0061695	cellular_component	transferase complex, transferring phosphorus-containing groups
B	0140535	cellular_component	intracellular protein-containing complex
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005666	cellular_component	RNA polymerase III complex
C	0005730	cellular_component	nucleolus
C	0005736	cellular_component	RNA polymerase I complex
C	0006360	biological_process	transcription by RNA polymerase I
C	0006361	biological_process	transcription initiation at RNA polymerase I promoter
C	0006362	biological_process	transcription elongation by RNA polymerase I
C	0006363	biological_process	termination of RNA polymerase I transcription
C	0006383	biological_process	transcription by RNA polymerase III
C	0006384	biological_process	transcription initiation at RNA polymerase III promoter
C	0006386	biological_process	termination of RNA polymerase III transcription
C	0042254	biological_process	ribosome biogenesis
C	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
C	0042797	biological_process	tRNA transcription by RNA polymerase III
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0001172	biological_process	RNA-templated transcription
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0003968	molecular_function	RNA-directed RNA polymerase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005665	cellular_component	RNA polymerase II, core complex
E	0005666	cellular_component	RNA polymerase III complex
E	0005736	cellular_component	RNA polymerase I complex
E	0006360	biological_process	transcription by RNA polymerase I
E	0006361	biological_process	transcription initiation at RNA polymerase I promoter
E	0006362	biological_process	transcription elongation by RNA polymerase I
E	0006363	biological_process	termination of RNA polymerase I transcription
E	0006366	biological_process	transcription by RNA polymerase II
E	0006367	biological_process	transcription initiation at RNA polymerase II promoter
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0006383	biological_process	transcription by RNA polymerase III
E	0006384	biological_process	transcription initiation at RNA polymerase III promoter
E	0006386	biological_process	termination of RNA polymerase III transcription
E	0042254	biological_process	ribosome biogenesis
E	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
E	0042797	biological_process	tRNA transcription by RNA polymerase III
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001172	biological_process	RNA-templated transcription
F	0003899	molecular_function	DNA-directed RNA polymerase activity
F	0003968	molecular_function	RNA-directed RNA polymerase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005736	cellular_component	RNA polymerase I complex
F	0005737	cellular_component	cytoplasm
F	0006360	biological_process	transcription by RNA polymerase I
F	0006361	biological_process	transcription initiation at RNA polymerase I promoter
F	0006362	biological_process	transcription elongation by RNA polymerase I
F	0006363	biological_process	termination of RNA polymerase I transcription
F	0006366	biological_process	transcription by RNA polymerase II
F	0006367	biological_process	transcription initiation at RNA polymerase II promoter
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006383	biological_process	transcription by RNA polymerase III
F	0006384	biological_process	transcription initiation at RNA polymerase III promoter
F	0006386	biological_process	termination of RNA polymerase III transcription
F	0042254	biological_process	ribosome biogenesis
F	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
F	0042797	biological_process	tRNA transcription by RNA polymerase III
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0003899	molecular_function	DNA-directed RNA polymerase activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005730	cellular_component	nucleolus
G	0005736	cellular_component	RNA polymerase I complex
G	0006360	biological_process	transcription by RNA polymerase I
G	0006361	biological_process	transcription initiation at RNA polymerase I promoter
G	0006362	biological_process	transcription elongation by RNA polymerase I
G	0006363	biological_process	termination of RNA polymerase I transcription
G	0042254	biological_process	ribosome biogenesis
G	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0001172	biological_process	RNA-templated transcription
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0003968	molecular_function	RNA-directed RNA polymerase activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005665	cellular_component	RNA polymerase II, core complex
H	0005666	cellular_component	RNA polymerase III complex
H	0005736	cellular_component	RNA polymerase I complex
H	0006360	biological_process	transcription by RNA polymerase I
H	0006361	biological_process	transcription initiation at RNA polymerase I promoter
H	0006362	biological_process	transcription elongation by RNA polymerase I
H	0006363	biological_process	termination of RNA polymerase I transcription
H	0006366	biological_process	transcription by RNA polymerase II
H	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0006368	biological_process	transcription elongation by RNA polymerase II
H	0006383	biological_process	transcription by RNA polymerase III
H	0006384	biological_process	transcription initiation at RNA polymerase III promoter
H	0006386	biological_process	termination of RNA polymerase III transcription
H	0042254	biological_process	ribosome biogenesis
H	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
H	0042797	biological_process	tRNA transcription by RNA polymerase III
I	0000122	biological_process	negative regulation of transcription by RNA polymerase II
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0003899	molecular_function	DNA-directed RNA polymerase activity
I	0005634	cellular_component	nucleus
I	0005730	cellular_component	nucleolus
I	0005736	cellular_component	RNA polymerase I complex
I	0006360	biological_process	transcription by RNA polymerase I
I	0006361	biological_process	transcription initiation at RNA polymerase I promoter
I	0006362	biological_process	transcription elongation by RNA polymerase I
I	0006363	biological_process	termination of RNA polymerase I transcription
I	0008270	molecular_function	zinc ion binding
I	0042254	biological_process	ribosome biogenesis
I	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
I	0046872	molecular_function	metal ion binding
I	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
I	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001172	biological_process	RNA-templated transcription
J	0003899	molecular_function	DNA-directed RNA polymerase activity
J	0003968	molecular_function	RNA-directed RNA polymerase activity
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005666	cellular_component	RNA polymerase III complex
J	0005730	cellular_component	nucleolus
J	0005736	cellular_component	RNA polymerase I complex
J	0006360	biological_process	transcription by RNA polymerase I
J	0006361	biological_process	transcription initiation at RNA polymerase I promoter
J	0006362	biological_process	transcription elongation by RNA polymerase I
J	0006363	biological_process	termination of RNA polymerase I transcription
J	0006366	biological_process	transcription by RNA polymerase II
J	0006367	biological_process	transcription initiation at RNA polymerase II promoter
J	0006368	biological_process	transcription elongation by RNA polymerase II
J	0006383	biological_process	transcription by RNA polymerase III
J	0006384	biological_process	transcription initiation at RNA polymerase III promoter
J	0006386	biological_process	termination of RNA polymerase III transcription
J	0008270	molecular_function	zinc ion binding
J	0042254	biological_process	ribosome biogenesis
J	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
J	0042797	biological_process	tRNA transcription by RNA polymerase III
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005666	cellular_component	RNA polymerase III complex
K	0005730	cellular_component	nucleolus
K	0005736	cellular_component	RNA polymerase I complex
K	0006351	biological_process	DNA-templated transcription
K	0006360	biological_process	transcription by RNA polymerase I
K	0006361	biological_process	transcription initiation at RNA polymerase I promoter
K	0006362	biological_process	transcription elongation by RNA polymerase I
K	0006363	biological_process	termination of RNA polymerase I transcription
K	0006383	biological_process	transcription by RNA polymerase III
K	0006384	biological_process	transcription initiation at RNA polymerase III promoter
K	0006386	biological_process	termination of RNA polymerase III transcription
K	0042254	biological_process	ribosome biogenesis
K	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
K	0042797	biological_process	tRNA transcription by RNA polymerase III
K	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001172	biological_process	RNA-templated transcription
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0003968	molecular_function	RNA-directed RNA polymerase activity
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005665	cellular_component	RNA polymerase II, core complex
L	0005666	cellular_component	RNA polymerase III complex
L	0005730	cellular_component	nucleolus
L	0005736	cellular_component	RNA polymerase I complex
L	0005737	cellular_component	cytoplasm
L	0005777	cellular_component	peroxisome
L	0006360	biological_process	transcription by RNA polymerase I
L	0006361	biological_process	transcription initiation at RNA polymerase I promoter
L	0006362	biological_process	transcription elongation by RNA polymerase I
L	0006363	biological_process	termination of RNA polymerase I transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0006367	biological_process	transcription initiation at RNA polymerase II promoter
L	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006383	biological_process	transcription by RNA polymerase III
L	0006384	biological_process	transcription initiation at RNA polymerase III promoter
L	0006386	biological_process	termination of RNA polymerase III transcription
L	0008270	molecular_function	zinc ion binding
L	0042254	biological_process	ribosome biogenesis
L	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
L	0042797	biological_process	tRNA transcription by RNA polymerase III
L	0046872	molecular_function	metal ion binding
M	0000428	cellular_component	DNA-directed RNA polymerase complex
M	0001188	biological_process	RNA polymerase I preinitiation complex assembly
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed RNA polymerase activity
M	0005634	cellular_component	nucleus
M	0005730	cellular_component	nucleolus
M	0005736	cellular_component	RNA polymerase I complex
M	0006360	biological_process	transcription by RNA polymerase I
M	0006361	biological_process	transcription initiation at RNA polymerase I promoter
M	0006362	biological_process	transcription elongation by RNA polymerase I
M	0006363	biological_process	termination of RNA polymerase I transcription
M	0008361	biological_process	regulation of cell size
M	0016740	molecular_function	transferase activity
M	0016779	molecular_function	nucleotidyltransferase activity
M	0042254	biological_process	ribosome biogenesis
M	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
N	0000428	cellular_component	DNA-directed RNA polymerase complex
N	0003899	molecular_function	DNA-directed RNA polymerase activity
N	0005634	cellular_component	nucleus
N	0005730	cellular_component	nucleolus
N	0005736	cellular_component	RNA polymerase I complex
N	0006360	biological_process	transcription by RNA polymerase I
N	0006361	biological_process	transcription initiation at RNA polymerase I promoter
N	0006362	biological_process	transcription elongation by RNA polymerase I
N	0006363	biological_process	termination of RNA polymerase I transcription
N	0042254	biological_process	ribosome biogenesis
N	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I

Functional Information from PROSITE/UniProt

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NAFRRimisevpsvAaeyVyffnNtSviqDEvLAhRIGLVP

Chain	Residue	Details
C	ASN65-PRO105

---

site_id	PS00466
Number of Residues	36
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpqCgneemnyhtLQLRSaDEGatvfytCts...CgykF

Chain	Residue	Details
I	CYS86-PHE121

---

site_id	PS01030
Number of Residues	25
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCLDCGDLLenpnavlgsnve..CsqC

Chain	Residue	Details
I	PHE9-CYS33

---

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE

Chain	Residue	Details
E	HIS147-GLU160

---

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ

Chain	Residue	Details
F	THR86-GLN100

---

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG

Chain	Residue	Details
J	ILE2-GLY11

---

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. IveEdHTLgNaLryvImknpdVefcgYsipHP

Chain	Residue	Details
K	ILE65-PRO96

---

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFSSrHGQKGV

Chain	Residue	Details
B	GLY914-VAL926

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Region: {"description":"Bridging helix","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	21
Details	Region: {"description":"Leucine-zipper"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	23
Details	Region: {"description":"Non-specific ssDNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	43
Details	Zinc finger: {"description":"C4-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10145","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1TWF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---