7OOB

Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)

Functional Information from GO Data

Chain	GOid	namespace	contents
a	0000012	biological_process	single strand break repair
a	0000109	cellular_component	nucleotide-excision repair complex
a	0000209	biological_process	protein polyubiquitination
a	0004842	molecular_function	ubiquitin-protein transferase activity
a	0005515	molecular_function	protein binding
a	0005634	cellular_component	nucleus
a	0005654	cellular_component	nucleoplasm
a	0006281	biological_process	DNA repair
a	0006283	biological_process	transcription-coupled nucleotide-excision repair
a	0006974	biological_process	DNA damage response
a	0006979	biological_process	response to oxidative stress
a	0009411	biological_process	response to UV
a	0010165	biological_process	response to X-ray
a	0016363	cellular_component	nuclear matrix
a	0016567	biological_process	protein ubiquitination
a	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
a	0032991	cellular_component	protein-containing complex
a	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
a	0044877	molecular_function	protein-containing complex binding
a	0051865	biological_process	protein autoubiquitination
a	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
a	0090262	biological_process	regulation of transcription-coupled nucleotide-excision repair
a	0097680	biological_process	double-strand break repair via classical nonhomologous end joining
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0000974	cellular_component	Prp19 complex
A	0001055	molecular_function	RNA polymerase II activity
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0005694	cellular_component	chromosome
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0031981	cellular_component	nuclear lumen
A	0032991	cellular_component	protein-containing complex
A	0033120	biological_process	positive regulation of RNA splicing
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046872	molecular_function	metal ion binding
A	1990841	molecular_function	promoter-specific chromatin binding
b	0000012	biological_process	single strand break repair
b	0000077	biological_process	DNA damage checkpoint signaling
b	0000303	biological_process	response to superoxide
b	0003677	molecular_function	DNA binding
b	0003678	molecular_function	DNA helicase activity
b	0003682	molecular_function	chromatin binding
b	0004386	molecular_function	helicase activity
b	0005515	molecular_function	protein binding
b	0005524	molecular_function	ATP binding
b	0005634	cellular_component	nucleus
b	0005654	cellular_component	nucleoplasm
b	0005730	cellular_component	nucleolus
b	0006281	biological_process	DNA repair
b	0006283	biological_process	transcription-coupled nucleotide-excision repair
b	0006284	biological_process	base-excision repair
b	0006290	biological_process	pyrimidine dimer repair
b	0006338	biological_process	chromatin remodeling
b	0006362	biological_process	transcription elongation by RNA polymerase I
b	0006366	biological_process	transcription by RNA polymerase II
b	0006974	biological_process	DNA damage response
b	0006979	biological_process	response to oxidative stress
b	0007254	biological_process	JNK cascade
b	0007399	biological_process	nervous system development
b	0008023	cellular_component	transcription elongation factor complex
b	0008094	molecular_function	ATP-dependent activity, acting on DNA
b	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
b	0009411	biological_process	response to UV
b	0009636	biological_process	response to toxic substance
b	0010165	biological_process	response to X-ray
b	0010224	biological_process	response to UV-B
b	0010332	biological_process	response to gamma radiation
b	0016787	molecular_function	hydrolase activity
b	0016887	molecular_function	ATP hydrolysis activity
b	0022008	biological_process	neurogenesis
b	0030182	biological_process	neuron differentiation
b	0030296	molecular_function	protein tyrosine kinase activator activity
b	0031175	biological_process	neuron projection development
b	0032784	biological_process	regulation of DNA-templated transcription elongation
b	0032786	biological_process	positive regulation of DNA-templated transcription, elongation
b	0034243	biological_process	regulation of transcription elongation by RNA polymerase II
b	0035264	biological_process	multicellular organism growth
b	0042262	biological_process	DNA protection
b	0045494	biological_process	photoreceptor cell maintenance
b	0045739	biological_process	positive regulation of DNA repair
b	0045943	biological_process	positive regulation of transcription by RNA polymerase I
b	0045944	biological_process	positive regulation of transcription by RNA polymerase II
b	0045945	biological_process	positive regulation of transcription by RNA polymerase III
b	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
b	0090734	cellular_component	site of DNA damage
b	0097680	biological_process	double-strand break repair via classical nonhomologous end joining
b	0110016	cellular_component	B-WICH complex
b	0140658	molecular_function	ATP-dependent chromatin remodeler activity
b	1905168	biological_process	positive regulation of double-strand break repair via homologous recombination
b	2001033	biological_process	negative regulation of double-strand break repair via nonhomologous end joining
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0000781	cellular_component	chromosome, telomeric region
B	0001055	molecular_function	RNA polymerase II activity
B	0001172	biological_process	RNA-templated transcription
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0003968	molecular_function	RNA-dependent RNA polymerase activity
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005665	cellular_component	RNA polymerase II, core complex
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
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	0046983	molecular_function	protein dimerization activity
d	0000781	cellular_component	chromosome, telomeric region
d	0003676	molecular_function	nucleic acid binding
d	0003677	molecular_function	DNA binding
d	0003684	molecular_function	damaged DNA binding
d	0005515	molecular_function	protein binding
d	0005615	cellular_component	extracellular space
d	0005634	cellular_component	nucleus
d	0005654	cellular_component	nucleoplasm
d	0005730	cellular_component	nucleolus
d	0005737	cellular_component	cytoplasm
d	0006281	biological_process	DNA repair
d	0006289	biological_process	nucleotide-excision repair
d	0006511	biological_process	ubiquitin-dependent protein catabolic process
d	0006915	biological_process	apoptotic process
d	0006974	biological_process	DNA damage response
d	0007056	biological_process	spindle assembly involved in female meiosis
d	0010498	biological_process	proteasomal protein catabolic process
d	0016055	biological_process	Wnt signaling pathway
d	0016567	biological_process	protein ubiquitination
d	0019076	biological_process	viral release from host cell
d	0030674	molecular_function	protein-macromolecule adaptor activity
d	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
d	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
d	0032991	cellular_component	protein-containing complex
d	0034644	biological_process	cellular response to UV
d	0035234	biological_process	ectopic germ cell programmed cell death
d	0035861	cellular_component	site of double-strand break
d	0042752	biological_process	regulation of circadian rhythm
d	0043066	biological_process	negative regulation of apoptotic process
d	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
d	0044725	biological_process	epigenetic programming in the zygotic pronuclei
d	0044877	molecular_function	protein-containing complex binding
d	0045070	biological_process	positive regulation of viral genome replication
d	0045722	biological_process	positive regulation of gluconeogenesis
d	0045732	biological_process	positive regulation of protein catabolic process
d	0046726	biological_process	positive regulation by virus of viral protein levels in host cell
d	0048511	biological_process	rhythmic process
d	0051093	biological_process	negative regulation of developmental process
d	0051702	biological_process	biological process involved in interaction with symbiont
d	0070062	cellular_component	extracellular exosome
d	0070914	biological_process	UV-damage excision repair
d	0071987	molecular_function	WD40-repeat domain binding
d	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
d	0097602	molecular_function	cullin family protein binding
d	0160072	molecular_function	ubiquitin ligase complex scaffold activity
d	1901990	biological_process	regulation of mitotic cell cycle phase transition
d	2000242	biological_process	negative regulation of reproductive process
D	0000166	molecular_function	nucleotide binding
D	0005634	cellular_component	nucleus
D	0005665	cellular_component	RNA polymerase II, core complex
D	0006352	biological_process	DNA-templated transcription initiation
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0030880	cellular_component	RNA polymerase complex
D	0031369	molecular_function	translation initiation factor binding
D	0044237	biological_process	cellular metabolic process
E	0001054	molecular_function	RNA polymerase I activity
E	0001055	molecular_function	RNA polymerase II activity
E	0001056	molecular_function	RNA polymerase III activity
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
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	0006351	biological_process	DNA-templated transcription
E	0006362	biological_process	transcription elongation by RNA polymerase I
E	0006366	biological_process	transcription by RNA polymerase II
E	0016591	cellular_component	RNA polymerase II, holoenzyme
E	0042797	biological_process	tRNA transcription by RNA polymerase III
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001650	cellular_component	fibrillar center
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
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	0006351	biological_process	DNA-templated transcription
F	0006366	biological_process	transcription by RNA polymerase II
G	0003676	molecular_function	nucleic acid binding
G	0006351	biological_process	DNA-templated transcription
G	0006352	biological_process	DNA-templated transcription initiation
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0005634	cellular_component	nucleus
H	0005665	cellular_component	RNA polymerase II, core complex
H	0006351	biological_process	DNA-templated transcription
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 5'-3' RNA polymerase activity
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005665	cellular_component	RNA polymerase II, core complex
I	0005730	cellular_component	nucleolus
I	0006283	biological_process	transcription-coupled nucleotide-excision repair
I	0006351	biological_process	DNA-templated transcription
I	0006366	biological_process	transcription by RNA polymerase II
I	0006367	biological_process	transcription initiation at RNA polymerase II promoter
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	0001054	molecular_function	RNA polymerase I activity
J	0001055	molecular_function	RNA polymerase II activity
J	0001056	molecular_function	RNA polymerase III activity
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005666	cellular_component	RNA polymerase III complex
J	0005736	cellular_component	RNA polymerase I complex
J	0006351	biological_process	DNA-templated transcription
J	0006360	biological_process	transcription by RNA polymerase I
J	0006366	biological_process	transcription by RNA polymerase II
J	0008270	molecular_function	zinc ion binding
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	0001055	molecular_function	RNA polymerase II activity
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0005634	cellular_component	nucleus
K	0005665	cellular_component	RNA polymerase II, core complex
K	0006351	biological_process	DNA-templated transcription
K	0006366	biological_process	transcription by RNA polymerase II
K	0016591	cellular_component	RNA polymerase II, holoenzyme
K	0046983	molecular_function	protein dimerization activity
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
L	0005634	cellular_component	nucleus
L	0005665	cellular_component	RNA polymerase II, core complex
L	0005666	cellular_component	RNA polymerase III complex
L	0005736	cellular_component	RNA polymerase I complex
L	0006351	biological_process	DNA-templated transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0008270	molecular_function	zinc ion binding
L	0046872	molecular_function	metal ion binding

Functional Information from PROSITE/UniProt

site_id	PS00018
Number of Residues	13
Details	EF_HAND_1 EF-hand calcium-binding domain. DNDPSDYVEqdDI

Chain	Residue	Details
C	ASP136-ILE148

---

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

Chain	Residue	Details
A	TYR1593-ALA1599
A	TYR1671-SER1677
A	TYR1678-SER1684
A	TYR1685-SER1691
A	TYR1692-SER1698
A	TYR1699-SER1705
A	TYR1706-SER1712
A	TYR1713-SER1719
A	TYR1720-SER1726
A	TYR1727-SER1733
A	TYR1734-SER1740
A	TYR1615-SER1621
A	TYR1741-ASN1747
A	TYR1748-ASN1754
A	TYR1755-SER1761
A	TYR1762-SER1768
A	TYR1769-ASN1775
A	TYR1776-ASN1782
A	TYR1783-SER1789
A	TYR1790-SER1796
A	TYR1797-SER1803
A	TYR1818-SER1824
A	TYR1622-SER1628
A	TYR1825-SER1831
A	TYR1832-LYS1838
A	TYR1839-SER1845
A	TYR1853-LYS1859
A	TYR1860-LYS1866
A	TYR1867-LYS1873
A	TYR1874-THR1880
A	TYR1888-THR1894
A	TYR1902-LYS1908
A	TYR1909-THR1915
A	TYR1629-ASN1635
A	TYR1916-LYS1922
A	TYR1923-THR1929
A	TYR1930-LYS1936
A	TYR1947-THR1953
A	TYR1636-SER1642
A	TYR1643-SER1649
A	TYR1650-SER1656
A	TYR1657-SER1663
A	TYR1664-SER1670

---

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH

Chain	Residue	Details
I	TYR112-HIS118

---

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

Chain	Residue	Details
C	ASN32-PRO72

---

site_id	PS00466
Number of Residues	38
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW

Chain	Residue	Details
I	CYS86-TRP123

---

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LATAsaDsRVKLWDV

Chain	Residue	Details
a	LEU202-VAL216
a	LEU260-SER274

---

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

Chain	Residue	Details
I	PHE16-CYS42

---

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

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. TkYErARvLGtRAlQ

Chain	Residue	Details
F	THR58-GLN72

---

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

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. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP

Chain	Residue	Details
K	ILE35-PRO66

---

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

Chain	Residue	Details
B	GLY932-THR944

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692

Chain	Residue	Details
a	SER390
a	SER391
a	SER392
A	ARG460
A	ASP499
A	ARG1416
A	ARG1421

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
d	LYS1067
A	ASP495
A	CYS74
A	CYS81
A	HIS84
A	CYS111
A	CYS114
A	CYS154
A	CYS184
A	ASN493

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q9ESW0

Chain	Residue	Details
d	THR1125
I	CYS20
I	CYS39
I	CYS42

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
d	LYS1121
b	LYS297
b	LYS448
b	LYS1054

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692

Chain	Residue	Details
b	SER429
A	SER1868
A	SER1875
A	SER1878
A	SER1882
A	SER1896
A	SER1899
A	SER1906
A	SER1913
A	SER1917
A	SER1920
b	SER430
A	SER1927
A	SER1931
A	SER1934
A	SER1843
A	SER1845
A	SER1849
A	SER1850
A	SER1857
A	SER1861
A	SER1864

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692

Chain	Residue	Details
b	SER486
b	SER489

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648

Chain	Residue	Details
b	SER1142

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163

Chain	Residue	Details
b	SER1348

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO3) => ECO:0000269|PubMed:26620705

Chain	Residue	Details
b	LYS205
A	THR1926
A	THR1929
A	THR1933
A	THR1854
A	THR1863
A	THR1870
A	THR1877
A	THR1885
A	THR1912
A	THR1915
A	THR1919

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
A	SER1847
b	LYS255

---

site_id	SWS_FT_FI11
Number of Residues	6
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P24928

Chain	Residue	Details
A	LYS1859
A	LYS1866
A	LYS1873
A	LYS1887
A	LYS1922
A	LYS1936

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P24928

Chain	Residue	Details
A	TYR1860
A	TYR1867
A	TYR1874
A	TYR1881
A	TYR1909
A	TYR1916
A	TYR1923
A	TYR1930

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P08775

Chain	Residue	Details
A	THR1894

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P08775

Chain	Residue	Details
A	LYS1908

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); by NEDD4 => ECO:0000250|UniProtKB:P24928

Chain	Residue	Details
A	LYS1268

---