6GMH

Structure of activated transcription complex Pol II-DSIF-PAF-SPT6

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
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	0000166	molecular_function	nucleotide binding
D	0006352	biological_process	DNA-templated transcription initiation
D	0030880	cellular_component	RNA polymerase complex
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	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	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	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	0046872	molecular_function	metal ion binding
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0006351	biological_process	DNA-templated transcription
J	0008270	molecular_function	zinc 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	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
M	0001825	biological_process	blastocyst formation
M	0003676	molecular_function	nucleic acid binding
M	0003677	molecular_function	DNA binding
M	0003723	molecular_function	RNA binding
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0006139	biological_process	nucleobase-containing compound metabolic process
M	0006366	biological_process	transcription by RNA polymerase II
M	0006368	biological_process	transcription elongation by RNA polymerase II
M	0006397	biological_process	mRNA processing
M	0008023	cellular_component	transcription elongation factor complex
M	0008380	biological_process	RNA splicing
M	0010793	biological_process	regulation of mRNA export from nucleus
M	0031491	molecular_function	nucleosome binding
M	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
M	0034728	biological_process	nucleosome organization
M	0042393	molecular_function	histone binding
M	0045191	biological_process	regulation of isotype switching
M	0050684	biological_process	regulation of mRNA processing
M	0051028	biological_process	mRNA transport
M	0051147	biological_process	regulation of muscle cell differentiation
M	0140673	biological_process	transcription elongation-coupled chromatin remodeling
Q	0006355	biological_process	regulation of DNA-templated transcription
U	0001650	cellular_component	fibrillar center
U	0001711	biological_process	endodermal cell fate commitment
U	0005515	molecular_function	protein binding
U	0005634	cellular_component	nucleus
U	0005654	cellular_component	nucleoplasm
U	0005813	cellular_component	centrosome
U	0006368	biological_process	transcription elongation by RNA polymerase II
U	0016055	biological_process	Wnt signaling pathway
U	0016593	cellular_component	Cdc73/Paf1 complex
U	0019827	biological_process	stem cell population maintenance
U	0031124	biological_process	mRNA 3'-end processing
U	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
U	0045638	biological_process	negative regulation of myeloid cell differentiation
U	0045944	biological_process	positive regulation of transcription by RNA polymerase II
U	1990269	molecular_function	RNA polymerase II C-terminal domain phosphoserine binding
V	0000122	biological_process	negative regulation of transcription by RNA polymerase II
V	0000993	molecular_function	RNA polymerase II complex binding
V	0001650	cellular_component	fibrillar center
V	0001711	biological_process	endodermal cell fate commitment
V	0003682	molecular_function	chromatin binding
V	0005515	molecular_function	protein binding
V	0005634	cellular_component	nucleus
V	0005654	cellular_component	nucleoplasm
V	0005737	cellular_component	cytoplasm
V	0006368	biological_process	transcription elongation by RNA polymerase II
V	0016020	cellular_component	membrane
V	0016055	biological_process	Wnt signaling pathway
V	0016593	cellular_component	Cdc73/Paf1 complex
V	0019827	biological_process	stem cell population maintenance
V	0031124	biological_process	mRNA 3'-end processing
V	0034504	biological_process	protein localization to nucleus
V	0043231	cellular_component	intracellular membrane-bounded organelle
V	0045638	biological_process	negative regulation of myeloid cell differentiation
V	0045944	biological_process	positive regulation of transcription by RNA polymerase II
V	0071222	biological_process	cellular response to lipopolysaccharide
V	1902808	biological_process	positive regulation of cell cycle G1/S phase transition
W	0000791	cellular_component	euchromatin
W	0005515	molecular_function	protein binding
W	0005634	cellular_component	nucleus
W	0005654	cellular_component	nucleoplasm
W	0005737	cellular_component	cytoplasm
W	0005829	cellular_component	cytosol
W	0006368	biological_process	transcription elongation by RNA polymerase II
W	0016055	biological_process	Wnt signaling pathway
W	0016593	cellular_component	Cdc73/Paf1 complex
W	0045638	biological_process	negative regulation of myeloid cell differentiation
W	0055087	cellular_component	Ski complex
W	0070478	biological_process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay
W	0072344	biological_process	rescue of stalled ribosome
Y	0000122	biological_process	negative regulation of transcription by RNA polymerase II
Y	0000993	molecular_function	RNA polymerase II complex binding
Y	0005515	molecular_function	protein binding
Y	0005634	cellular_component	nucleus
Y	0005654	cellular_component	nucleoplasm
Y	0006355	biological_process	regulation of DNA-templated transcription
Y	0006368	biological_process	transcription elongation by RNA polymerase II
Y	0008270	molecular_function	zinc ion binding
Y	0032044	cellular_component	DSIF complex
Y	0032785	biological_process	negative regulation of DNA-templated transcription, elongation
Y	0032786	biological_process	positive regulation of DNA-templated transcription, elongation
Y	0034243	biological_process	regulation of transcription elongation by RNA polymerase II
Y	0034244	biological_process	negative regulation of transcription elongation by RNA polymerase II
Y	0045944	biological_process	positive regulation of transcription by RNA polymerase II
Y	0046872	molecular_function	metal ion binding
Y	0046982	molecular_function	protein heterodimerization activity
Y	0140673	biological_process	transcription elongation-coupled chromatin remodeling
Z	0000122	biological_process	negative regulation of transcription by RNA polymerase II
Z	0003682	molecular_function	chromatin binding
Z	0003723	molecular_function	RNA binding
Z	0003729	molecular_function	mRNA binding
Z	0005515	molecular_function	protein binding
Z	0005634	cellular_component	nucleus
Z	0005654	cellular_component	nucleoplasm
Z	0006354	biological_process	DNA-templated transcription elongation
Z	0006357	biological_process	regulation of transcription by RNA polymerase II
Z	0006368	biological_process	transcription elongation by RNA polymerase II
Z	0016239	biological_process	positive regulation of macroautophagy
Z	0019899	molecular_function	enzyme binding
Z	0032044	cellular_component	DSIF complex
Z	0032784	biological_process	regulation of DNA-templated transcription elongation
Z	0032785	biological_process	negative regulation of DNA-templated transcription, elongation
Z	0032786	biological_process	positive regulation of DNA-templated transcription, elongation
Z	0034243	biological_process	regulation of transcription elongation by RNA polymerase II
Z	0045944	biological_process	positive regulation of transcription by RNA polymerase II
Z	0046982	molecular_function	protein heterodimerization activity
Z	0140673	biological_process	transcription elongation-coupled chromatin remodeling

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 2001

Chain	Residue
A	CYS71
A	CYS74
A	CYS81
A	PRO82
A	HIS84

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN A 2002

Chain	Residue
A	CYS111
A	CYS114
A	LYS116
A	TYR187

---

site_id	AC3
Number of Residues	4
Details	binding site for residue MG A 2003

Chain	Residue
A	ASP495
A	ASP497
A	ASP499
P	U46

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN B 1201

Chain	Residue
B	CYS1119
B	CYS1122
B	CYS1137
B	CYS1140

---

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN C 301

Chain	Residue
C	CYS88
C	CYS90
C	CYS94
C	CYS97

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN I 201

Chain	Residue
I	CYS17
I	CYS20
I	CYS39
I	CYS42

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN I 202

Chain	Residue
I	CYS86
I	CYS89
I	CYS114
I	CYS119

---

site_id	AC8
Number of Residues	4
Details	binding site for residue ZN J 101

Chain	Residue
J	CYS7
J	CYS10
J	CYS44
J	CYS45

---

site_id	AC9
Number of Residues	5
Details	binding site for residue ZN L 101

Chain	Residue
L	CYS19
L	CYS22
L	CYS36
L	GLU38
L	CYS39

---

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN Y 201

Chain	Residue
Y	CYS16
Y	CYS19
Y	CYS33
Y	CYS36

---

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. AASSslDaHIRLWDL

Chain	Residue	Details
W	ALA79-LEU93

---

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	2
Details	BINDING: BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK

Chain	Residue	Details
Z	LYS579
Z	ARG619

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O55201

Chain	Residue	Details
Z	SER32
Z	SER36
U	SER767
Y	CYS36

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
Z	SER666
U	SER680
V	LYS492
U	SER741
U	SER749

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: Omega-N-methylarginine; by PRMT1; alternate => ECO:0000269|PubMed:12718890

Chain	Residue	Details
Z	ARG681
Z	ARG696
I	CYS114
I	CYS119

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
Z	SER686
Z	SER789
Z	SER804

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000269|PubMed:12718890

Chain	Residue	Details
Z	ARG698
Q	SER1041
Q	SER1043
Q	SER1081
Q	SER1085

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O55201

Chain	Residue	Details
Z	LYS718
M	GLU1679

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by CDK9 => ECO:0000269|PubMed:10757782

Chain	Residue	Details
Z	THR775
Z	THR784

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
Z	THR791
Z	THR806

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163

Chain	Residue	Details
Z	THR1034
M	ARG1531

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733

Chain	Residue	Details
Z	LYS143

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
U	SER823
Z	LYS1037

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER825

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER829

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	TYR1135
M	ILE1706

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692

Chain	Residue	Details
U	SER1136
U	SER1137

---

site_id	SWS_FT_FI17
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648

Chain	Residue	Details
U	SER1143

---

site_id	SWS_FT_FI18
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332

Chain	Residue	Details
U	THR1158

---

site_id	SWS_FT_FI19
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER1159

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18318008, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER1187

---