Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8OF0

Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase 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	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0016779	molecular_function	nucleotidyltransferase activity
A	0031981	cellular_component	nuclear lumen
A	0032991	cellular_component	protein-containing complex
A	0046872	molecular_function	metal ion binding
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	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005665	cellular_component	RNA polymerase II, core complex
D	0005829	cellular_component	cytosol
D	0006352	biological_process	DNA-templated transcription initiation
D	0006366	biological_process	transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0016607	cellular_component	nuclear speck
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	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0000932	cellular_component	P-body
G	0003676	molecular_function	nucleic acid binding
G	0003697	molecular_function	single-stranded DNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0005634	cellular_component	nucleus
G	0005665	cellular_component	RNA polymerase II, core complex
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	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	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	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
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
M	0005515	molecular_function	protein binding
M	0005615	cellular_component	extracellular space
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0006357	biological_process	regulation of transcription by RNA polymerase II
M	0006366	biological_process	transcription by RNA polymerase II
M	0006367	biological_process	transcription initiation at RNA polymerase II promoter
M	0006368	biological_process	transcription elongation by RNA polymerase II
M	0070449	cellular_component	elongin complex
M	0090734	cellular_component	site of DNA damage
O	0001222	molecular_function	transcription corepressor binding
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005829	cellular_component	cytosol
O	0006357	biological_process	regulation of transcription by RNA polymerase II
O	0006367	biological_process	transcription initiation at RNA polymerase II promoter
O	0006511	biological_process	ubiquitin-dependent protein catabolic process
O	0016567	biological_process	protein ubiquitination
O	0030674	molecular_function	protein-macromolecule adaptor activity
O	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
O	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
O	0070449	cellular_component	elongin complex
O	0140958	biological_process	target-directed miRNA degradation
Q	0001222	molecular_function	transcription corepressor binding
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005654	cellular_component	nucleoplasm
Q	0005829	cellular_component	cytosol
Q	0006367	biological_process	transcription initiation at RNA polymerase II promoter
Q	0006368	biological_process	transcription elongation by RNA polymerase II
Q	0016567	biological_process	protein ubiquitination
Q	0030891	cellular_component	VCB complex
Q	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
Q	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
Q	0031625	molecular_function	ubiquitin protein ligase binding
Q	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Q	0065003	biological_process	protein-containing complex assembly
Q	0070449	cellular_component	elongin complex
Q	0140958	biological_process	target-directed miRNA degradation
S	0001825	biological_process	blastocyst formation
S	0003676	molecular_function	nucleic acid binding
S	0003677	molecular_function	DNA binding
S	0003723	molecular_function	RNA binding
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005654	cellular_component	nucleoplasm
S	0006139	biological_process	nucleobase-containing compound metabolic process
S	0006366	biological_process	transcription by RNA polymerase II
S	0006368	biological_process	transcription elongation by RNA polymerase II
S	0006397	biological_process	mRNA processing
S	0008023	cellular_component	transcription elongation factor complex
S	0008380	biological_process	RNA splicing
S	0010793	biological_process	regulation of mRNA export from nucleus
S	0031491	molecular_function	nucleosome binding
S	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
S	0034728	biological_process	nucleosome organization
S	0042393	molecular_function	histone binding
S	0045191	biological_process	regulation of isotype switching
S	0050684	biological_process	regulation of mRNA processing
S	0051028	biological_process	mRNA transport
S	0051147	biological_process	regulation of muscle cell differentiation
S	0140673	biological_process	transcription elongation-coupled chromatin remodeling

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
I	CYS86-TRP123

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

Chain	Residue	Details
B	GLY1009-THR1021

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	TYR1615-SER1621
A	TYR1622-SER1628
A	TYR1629-ASN1635
A	TYR1636-SER1642
A	TYR1643-SER1649
A	TYR1650-SER1656
A	TYR1657-SER1663
A	TYR1664-SER1670
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	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	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	TYR1916-LYS1922
A	TYR1923-THR1929
A	TYR1930-LYS1936
A	TYR1947-THR1953

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

Chain	Residue	Details
I	PHE16-CYS42

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: N-acetylserine => ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:21406692

Chain	Residue	Details
A	LYS346
A	ARG358
A	ARG460
A	ASP499
A	ARG1416
A	ARG1421
S	SER2

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21406692

Chain	Residue	Details
S	SER12
A	CYS81
A	HIS84
A	CYS111
A	CYS114
A	CYS154
A	CYS184
A	ASN493
A	ASP495
S	SER7

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19690332

Chain	Residue	Details
I	CYS39
I	CYS42
S	SER73
Q	SER111

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q62383

Chain	Residue	Details
I	CYS114
I	CYS119
S	SER78
S	SER91

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163, ECO:0007744\|PubMed:24275569

Chain	Residue	Details
A	SER217
A	SER1843
A	SER1845
A	SER1849
A	SER1850
A	SER1857
A	SER1861
A	SER1864
A	SER1868
A	SER1875
A	SER1878
A	SER1882
A	SER1896
A	SER1899
A	SER1906
A	SER1913
A	SER1917
A	SER1920
A	SER1927
A	SER1931
A	SER1934
S	SER125

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648

Chain	Residue	Details
S	SER267

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
S	LYS743
S	LYS1676

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0007744\|PubMed:24275569

Chain	Residue	Details
S	TYR1515

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
S	THR1523
A	THR1854
A	THR1912
A	THR1915
A	THR1919
A	THR1926
A	THR1929
A	THR1933
A	THR1863
A	THR1870
A	THR1877
A	THR1885

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
S	SER1526
S	SER1528

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:20068231

Chain	Residue	Details
S	THR1532
A	LYS1866
A	LYS1873
A	LYS1887
A	LYS1922
A	LYS1936

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18220336, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
S	SER1535
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:0007744\|PubMed:18220336, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:19690332

Chain	Residue	Details
S	THR1539

site_id	SWS_FT_FI14
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19690332

Chain	Residue	Details
S	THR1697

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:20068231

Chain	Residue	Details
S	SER1701
S	SER1703

site_id	SWS_FT_FI16
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q62383

Chain	Residue	Details
S	THR1709

site_id	SWS_FT_FI17
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18220336, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:20068231

Chain	Residue	Details
S	THR1718

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