8QSZ

Structure of s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0000785	cellular_component	chromatin
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0006325	biological_process	chromatin organization
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0006367	biological_process	transcription initiation at RNA polymerase II promoter
A	0006368	biological_process	transcription elongation by RNA polymerase II
A	0006369	biological_process	termination of RNA polymerase II transcription
A	0006370	biological_process	7-methylguanosine mRNA capping
A	0016591	cellular_component	RNA polymerase II, holoenzyme
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0030643	biological_process	intracellular phosphate ion homeostasis
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042789	biological_process	mRNA transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0140463	molecular_function	chromatin-protein adaptor activity
A	0180034	biological_process	co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005665	cellular_component	RNA polymerase II, core complex
B	0005721	cellular_component	pericentric heterochromatin
B	0005829	cellular_component	cytosol
B	0006351	biological_process	DNA-templated transcription
B	0006354	biological_process	DNA-templated transcription elongation
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0016591	cellular_component	RNA polymerase II, holoenzyme
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0031047	biological_process	regulatory ncRNA-mediated gene silencing
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
B	0140727	biological_process	siRNA-mediated pericentric heterochromatin formation
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0000785	cellular_component	chromatin
C	0003677	molecular_function	DNA binding
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	0005665	cellular_component	RNA polymerase II, core complex
C	0005829	cellular_component	cytosol
C	0006351	biological_process	DNA-templated transcription
C	0006366	biological_process	transcription by RNA polymerase II
C	0006367	biological_process	transcription initiation at RNA polymerase II promoter
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0016591	cellular_component	RNA polymerase II, holoenzyme
C	0046983	molecular_function	protein dimerization activity
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	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	0005829	cellular_component	cytosol
E	0006351	biological_process	DNA-templated transcription
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	0016591	cellular_component	RNA polymerase II, holoenzyme
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	0003677	molecular_function	DNA binding
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	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	0005829	cellular_component	cytosol
F	0006351	biological_process	DNA-templated transcription
F	0006354	biological_process	DNA-templated transcription elongation
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	0006384	biological_process	transcription initiation at RNA polymerase III promoter
F	0006386	biological_process	termination of RNA polymerase III transcription
F	0016591	cellular_component	RNA polymerase II, holoenzyme
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	0000932	cellular_component	P-body
G	0000956	biological_process	nuclear-transcribed mRNA catabolic process
G	0003676	molecular_function	nucleic acid binding
G	0003697	molecular_function	single-stranded DNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005665	cellular_component	RNA polymerase II, core complex
G	0005829	cellular_component	cytosol
G	0006351	biological_process	DNA-templated transcription
G	0006352	biological_process	DNA-templated transcription initiation
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0006368	biological_process	transcription elongation by RNA polymerase II
G	0010590	biological_process	regulation of septum digestion after cytokinesis
G	0016591	cellular_component	RNA polymerase II, holoenzyme
G	0031369	molecular_function	translation initiation factor binding
G	0045948	biological_process	positive regulation of translational initiation
G	0060213	biological_process	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
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	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	0005829	cellular_component	cytosol
H	0006351	biological_process	DNA-templated transcription
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	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0006368	biological_process	transcription elongation by RNA polymerase II
H	0006384	biological_process	transcription initiation at RNA polymerase III promoter
H	0006386	biological_process	termination of RNA polymerase III transcription
H	0016591	cellular_component	RNA polymerase II, holoenzyme
H	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001193	biological_process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
I	0003676	molecular_function	nucleic acid binding
I	0003899	molecular_function	DNA-directed RNA polymerase activity
I	0005634	cellular_component	nucleus
I	0005665	cellular_component	RNA polymerase II, core complex
I	0005730	cellular_component	nucleolus
I	0005829	cellular_component	cytosol
I	0006283	biological_process	transcription-coupled nucleotide-excision repair
I	0006351	biological_process	DNA-templated transcription
I	0006367	biological_process	transcription initiation at RNA polymerase II promoter
I	0006368	biological_process	transcription elongation by RNA polymerase II
I	0008270	molecular_function	zinc ion binding
I	0016591	cellular_component	RNA polymerase II, holoenzyme
I	0046872	molecular_function	metal ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001172	biological_process	RNA-templated transcription
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed RNA polymerase activity
J	0003968	molecular_function	RNA-directed RNA polymerase activity
J	0005634	cellular_component	nucleus
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	0005829	cellular_component	cytosol
J	0006351	biological_process	DNA-templated transcription
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	0016591	cellular_component	RNA polymerase II, holoenzyme
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	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0005634	cellular_component	nucleus
K	0005665	cellular_component	RNA polymerase II, core complex
K	0005829	cellular_component	cytosol
K	0006351	biological_process	DNA-templated transcription
K	0006366	biological_process	transcription by RNA polymerase II
K	0006367	biological_process	transcription initiation at RNA polymerase II promoter
K	0006368	biological_process	transcription elongation by RNA polymerase II
K	0016591	cellular_component	RNA polymerase II, holoenzyme
K	0046983	molecular_function	protein dimerization activity
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001172	biological_process	RNA-templated transcription
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0003968	molecular_function	RNA-directed RNA polymerase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
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	0005829	cellular_component	cytosol
L	0006351	biological_process	DNA-templated transcription
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	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
L	0046872	molecular_function	metal ion binding
X	0000448	biological_process	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
X	0000956	biological_process	nuclear-transcribed mRNA catabolic process
X	0003676	molecular_function	nucleic acid binding
X	0003723	molecular_function	RNA binding
X	0004518	molecular_function	nuclease activity
X	0004527	molecular_function	exonuclease activity
X	0004534	molecular_function	5'-3' RNA exonuclease activity
X	0005515	molecular_function	protein binding
X	0005634	cellular_component	nucleus
X	0006139	biological_process	nucleobase-containing compound metabolic process
X	0006351	biological_process	DNA-templated transcription
X	0006353	biological_process	DNA-templated transcription termination
X	0006364	biological_process	rRNA processing
X	0006397	biological_process	mRNA processing
X	0016787	molecular_function	hydrolase activity
X	0051984	biological_process	positive regulation of chromosome segregation
X	0071028	biological_process	nuclear mRNA surveillance
X	0090730	cellular_component	Las1 complex
X	0180037	biological_process	rapid tRNA decay
Y	0000785	cellular_component	chromatin
Y	0003711	molecular_function	transcription elongation factor activity
Y	0003729	molecular_function	mRNA binding
Y	0005515	molecular_function	protein binding
Y	0005634	cellular_component	nucleus
Y	0006325	biological_process	chromatin organization
Y	0006351	biological_process	DNA-templated transcription
Y	0006354	biological_process	DNA-templated transcription elongation
Y	0006355	biological_process	regulation of DNA-templated transcription
Y	0006357	biological_process	regulation of transcription by RNA polymerase II
Y	0006368	biological_process	transcription elongation by RNA polymerase II
Y	0006397	biological_process	mRNA processing
Y	0015035	molecular_function	protein-disulfide reductase activity
Y	0032044	cellular_component	DSIF complex
Y	0032784	biological_process	regulation of DNA-templated transcription elongation
Y	0032991	cellular_component	protein-containing complex
Y	0140463	molecular_function	chromatin-protein adaptor activity

Functional Information from PROSITE/UniProt

site_id	PS00115
Number of Residues	7
Details	RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPS

Chain	Residue	Details
A	TYR1578-SER1584
A	TYR1648-SER1654
A	TYR1655-SER1661
A	TYR1662-SER1668
A	TYR1669-SER1675
A	TYR1676-SER1682
A	TYR1683-SER1689
A	TYR1690-SER1696
A	TYR1697-SER1703
A	TYR1704-SER1710
A	TYR1711-SER1717
A	TYR1585-SER1591
A	TYR1718-SER1724
A	TYR1725-SER1731
A	TYR1732-SER1738
A	TYR1739-SER1745
A	TYR1746-SER1752
A	TYR1592-SER1598
A	TYR1599-SER1605
A	TYR1613-SER1619
A	TYR1620-SER1626
A	TYR1627-SER1633
A	TYR1634-SER1640
A	TYR1641-SER1647

---

site_id	PS00194
Number of Residues	19
Details	THIOREDOXIN_1 Thioredoxin family active site. LVdFWaeWCGPCKmIapiL

Chain	Residue	Details
Y	LEU-98-LEU-80

---

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

Chain	Residue	Details
C	ASN30-PRO70

---

site_id	PS00466
Number of Residues	36
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CprChqheavfyqTHSRRgDTMmtliyvCvh...CgfaF

Chain	Residue	Details
I	CYS75-PHE110

---

site_id	PS01030
Number of Residues	27
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. YCIECNNMLypredkvdrvlrlaCrnC

Chain	Residue	Details
I	TYR6-CYS32

---

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

Chain	Residue	Details
E	HIS142-GLU155

---

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	THR76-GLN90

---

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

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. LekEdHTLaNmLanqLlsderVlfagYkvpHP

Chain	Residue	Details
K	LEU34-PRO65

---

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

Chain	Residue	Details
B	GLY966-THR978

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Region: {"description":"Bridging helix"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P04050","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P04050","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	21
Details	Zinc finger: {"description":"C4-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	9
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18257517","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	22
Details	Region: {"description":"Non-specific ssDNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	45
Details	Zinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10145","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00472","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19458260","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3H0G","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	27
Details	Domain: {"description":"KOW 3"}

Chain

Residue

Details

---